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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AND TRIGLU-5-FORMYL-TETRAHYDROFOLATE
 
Authors :  T. F. Fu, J. N. Scarsdale, G. Kazanina, V. Schirch, H. T. Wright
Date :  16 May 02  (Deposition) - 04 Feb 03  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Asymmetric Tetramer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. F. Fu, J. N. Scarsdale, G. Kazanina, V. Schirch, H. T. Wright
Location Of The Pteroylpolyglutamate Binding Site On Rabbit Cytosolic Serine Hydroxymethyltransferase
J. Biol. Chem. V. 278 2645 2003
PubMed-ID: 12438316  |  Reference-DOI: 10.1074/JBC.M210649200

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 22B(+)
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: SERINE METHYLASE, GLYCINE HYDROXYMETHYLTRANSFERASE, SHMT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2GOL4Ligand/IonGLYCEROL
3PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4TGF2Ligand/Ion2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAMINO)-4-CARBOXY-BUTYRYLAMINO]-PENTANEDIOIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:97 , GLY A:98 , SER A:99 , HIS A:126 , THR A:174 , SER A:175 , ASP A:200 , ALA A:202 , HIS A:203 , THR A:226 , HIS A:228 , LYS A:229 , GLY A:420B , HOH A:506 , HOH A:515 , TYR B:55 , GLY B:262 , GLY B:263BINDING SITE FOR RESIDUE PLP A 419A
02AC2SOFTWARESER A:35 , HIS A:126 , SER A:175 , LYS A:229 , ARG A:363 , PLP A:419A , HOH A:515 , TYR B:65BINDING SITE FOR RESIDUE GLY A 420B
03AC3SOFTWARESER C:97 , GLY C:98 , SER C:99 , HIS C:126 , THR C:174 , SER C:175 , ASP C:200 , ALA C:202 , HIS C:203 , THR C:226 , HIS C:228 , LYS C:229 , GLY C:420B , TYR D:55 , GLY D:262 , GLY D:263BINDING SITE FOR RESIDUE PLP C 419A
04AC4SOFTWARESER C:35 , SER C:175 , HIS C:203 , LYS C:229 , ARG C:363 , PLP C:419A , TYR D:65BINDING SITE FOR RESIDUE GLY C 420B
05AC5SOFTWARETYR A:55 , GLY A:262 , GLY A:263 , SER B:97 , GLY B:98 , SER B:99 , HIS B:126 , THR B:174 , SER B:175 , ASP B:200 , ALA B:202 , HIS B:203 , THR B:226 , HIS B:228 , LYS B:229BINDING SITE FOR RESIDUE PLP B 419A
06AC6SOFTWAREGLU A:57 , TYR A:64 , TYR A:65 , PHE A:257 , LEU B:121 , GLY B:124 , GLY B:125 , HIS B:126 , LEU B:127 , LYS B:134A , SER B:175 , ASN B:345 , LEU B:357 , HOH B:739BINDING SITE FOR RESIDUE TGF B 420C
07AC7SOFTWARETYR C:55 , GLY C:262 , GLY C:263 , SER D:97 , GLY D:98 , SER D:99 , HIS D:126 , THR D:174 , SER D:175 , ASP D:200 , ALA D:202 , HIS D:203 , THR D:226 , HIS D:228 , LYS D:229BINDING SITE FOR RESIDUE PLP D 419A
08AC8SOFTWAREGLU C:57 , TYR C:64 , TYR C:65 , GLY D:124 , GLY D:125 , HIS D:126 , LEU D:127 , LYS D:134A , SER D:175 , CYS D:176 , GLY D:331 , ASN D:345 , LYS D:346 , ASN D:347 , ALA D:356 , LEU D:357 , PRO D:359 , HOH D:740BINDING SITE FOR RESIDUE TGF D 420F
09AC9SOFTWAREASP D:182BINDING SITE FOR RESIDUE GOL D 421
10BC1SOFTWAREPHE B:418J , ASP C:156 , HOH C:679BINDING SITE FOR RESIDUE GOL C 421
11BC2SOFTWARELEU B:181 , ASP B:182BINDING SITE FOR RESIDUE GOL B 421
12BC3SOFTWARESER A:49 , ILE B:19 , PRO B:418H , PHE B:418JBINDING SITE FOR RESIDUE GOL B 422

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LS3)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:257 -Pro A:258
2Phe B:257 -Pro B:258
3Gly B:396A-Pro B:396B
4Phe C:257 -Pro C:258
5Phe D:257 -Pro D:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LS3)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYC_RABIT249-265
 
 
 		  4A:221-237
B:221-237
C:221-237
D:221-237

(-) Exons   (0, 0)

(no "Exon" information available for 1LS3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:465
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:472
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
          GLYC_RABIT     13 ALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF  484
               SCOP domains d1ls3a_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -----------------1ls3A01 A:12-36,A:290-4181ls3A02 A:37-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1ls3A01 A:12-36,A:290-418 Aspartate Aminotransferase, domain 1                                                                                   ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..hh.hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh........hhhhhh.eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee.......-------..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhh..ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ls3 A  -10 ALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVD-------LYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 418J
                                   ||2    ||  14        24        34        44        54        64        74        84     |||91|      100       110  |||  120       130    |||137 |  |  145    |  154       164       174       184       194       204       214       224       234       244|||||    -  |  |252A       262       272       282       292       302       312       322       332       342       352|      363       373 ||   |383       392  ||| 396C   ||||402  ||  |409  |    416  ||||418H||
                                  -3|     7|                                                                             89A||  |                  112A||                134A|| 138A  |      149A                                                                                            244A||||     248  ||  |                                                                                                 352|                 374A| 378||      391A   |||  |||  399C|  404A|  |  411A 415A|   ||||418H||
                                    1     10                                                                              89B|  |                    113|                 134B|    140A                                                                                                       244B|||       250A|  |                                                                                                  354                  374B  380|          394A||  |||   399D   404C  |        415B   |||||418I|
                                                                                                                           89C  |                     115                  134C                                                                                                                244C||        250B  |                                                                                                                              382           394B|  |||   ||        406A            418A|||||418J
                                                                                                                              91A                                                                                                                                                               244D|           252A                                                                                                                                             394C  |||   ||                         418B|||||   
                                                                                                                                                                                                                                                                                                 244E                                                                                                                                                               396A||   ||                          418C||||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     396B|   ||                           418D|||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      396C   ||                            418E||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          399A|                             418F|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           399B                              418G   


Chain B from PDB  Type:PROTEIN  Length:455
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:470
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
          GLYC_RABIT     15 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF  484
               SCOP domains d1ls3b_ B: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------1ls3B01 B:12-36,B:290-4181ls3B02 B:37-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1ls3B01 B:12-36,B:290-418 Aspartate  Aminotransferase, domain  1                                                                                 ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh........hhhhhh.eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee........-------.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee..-...hhhhhhhhhhhh.ee.eee....-.--....eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..............----hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ls3 B   -8 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDP-------YNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLR-KGTDGGRAEKVLEACSIACNKNTCPG-K--LRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKE----DEKHQRAVRALRQEVESFAALFPLPGLPGF 418J
                                 ||  4  ||    16        26        36        46        56        66        76        86   |||  92       102       112|||    122       132  ||| 138A  |    147  |    156       166       176       186       196       206       216       226       236      244B||||     - | ||  254       264       274       284       294       304       314       324 |     334       344      | |- |     365      374A|   |||385      |394|||  ||398 |||||   -||  |  411|    ||418||||||418J
                                -3|     7|                                                                             89A||  |                  112A||                134A|| 138A  |      149A                                                                                            244A|||||     249 ||  |                                                                     324 |                      351 |  |              374A| 378||      391A   |||  |||  399C|| 404A|  |  411A 415A|   ||||418H||
                                  1     10                                                                              89B|  |                    113|                 134B|    140A                                                                                                       244B||||      250A|  |                                                                       326                        354  |               374B  380|          394A||  |||   399D|  404B  |        415B   |||||418I|
                                                                                                                         89C  |                     115                  134C                                                                                                                244C|||       250B  |                                                                                                     357                      382           394B|  |||   ||400     406A            418A|||||418J
                                                                                                                            91A                                                                                                                                                               244D||          252A                                                                                                                                             394C  |||   ||                         418B|||||   
                                                                                                                                                                                                                                                                                               244E|                                                                                                                                                              396A||   ||                          418C||||   
                                                                                                                                                                                                                                                                                                244F                                                                                                                                                               396B|   ||                           418D|||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    396C   ||                            418E||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        399A|                             418F|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         399B                              418G   


Chain C from PDB  Type:PROTEIN  Length:466
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 484 
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482 | 
          GLYC_RABIT     13 ALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF-    -
               SCOP domains d1ls3c_ C: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------------1ls3C01 C:12-36,C:290-4181ls3C02 C:37-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1ls3C01 C:12-36,C:290-418 Aspartate Aminotransferase, domain 1                                                                                   ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh..hh.hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh........hhhhhh.eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee....-------.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhh..ee.eee............eeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ls3 C  -10 ALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVR-------KEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGFG 420B
                                   ||2    ||  14        24        34        44        54        64        74        84     |||91|      100       110  |||  120       130    |||137 |  |  145    |  154       164       174       184       194       204       214       224       234       244||     245     |252A       262       272       282       292       302       312       322       332       342       352|      363       373 ||   |383       392  ||| 396C   ||||402  ||  |409  |    416  ||||418H|||
                                  -3|     7|                                                                             89A||  |                  112A||                134A|| 138A  |      149A                                                                                            244A|     245  250A|  |                                                                                                 352|                 374A| 378||      391A   |||  |||  399C|  404A|  |  411A 415A|   ||||418H|||
                                    1     10                                                                              89B|  |                    113|                 134B|    140A                                                                                                       244B           250B  |                                                                                                  354                  374B  380|          394A||  |||   399D   404C  |        415B   |||||418I||
                                                                                                                           89C  |                     115                  134C                                                                                                                                 252A                                                                                                                              382           394B|  |||   ||        406A            418A|||||418J|
                                                                                                                              91A                                                                                                                                                                                                                                                                                                                                394C  |||   ||                         418B|||||420B
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    396A||   ||                          418C||||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     396B|   ||                           418D|||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      396C   ||                            418E||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          399A|                             418F|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           399B                              418G    


Chain D from PDB  Type:PROTEIN  Length:456
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:468
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476        
          GLYC_RABIT     17 SHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF  484
               SCOP domains d1ls3d_ D: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------1ls3D01 D:12-36,D:290-4181ls3D02 D:37-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1ls3D01 D:12-36,D:290-418 Aspartate Aminotransferase, domain 1                                                                                   ---------- CATH domains
           Pfam domains (1) ---------SHMT-1ls3D01 D:6-386                                                                                                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------SHMT-1ls3D02 D:6-386                                                                                                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------SHMT-1ls3D03 D:6-386                                                                                                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------SHMT-1ls3D04 D:6-386                                                                                                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ........hh.hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...............eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee...------------.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee......hhhhhhhhhhhh.ee.ee..............eeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1ls3 D   -6 SHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGV------------YNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 418J
                               ||    6||      18        28        38        48        58        68        78        88 |||  | 94       104       113|      124       134|||    140|      149|      158       168       178       188       198       208       218       228       238      |  -       249 ||  | 256       266       276       286       296       306       316       326       336       346     ||357       367       375  |||  387    | 394B|  |||399A|||   404C  |    412   || 418B||||||||
                              -3|     7|                                                                             89A||  |                  112A||                134A|| 138A  |      149A                                                                                            244A          249 ||  |                                                                                                 352|                 374A| 378||      391A   |||  |||  399C|  404A|  |  411A 415A|   ||||418H||
                                1     10                                                                              89B|  |                    113|                 134B|    140A                                                                                                                     250A|  |                                                                                                  354                  374B  380|          394A||  |||   399D   404C  |        415B   |||||418I|
                                                                                                                       89C  |                     115                  134C                                                                                                                              250B  |                                                                                                                              382           394B|  |||   ||        406A            418A|||||418J
                                                                                                                          91A                                                                                                                                                                               252A                                                                                                                                             394C  |||   ||                         418B|||||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                396A||   ||                          418C||||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 396B|   ||                           418D|||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  396C   ||                            418E||   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      399A|                             418F|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       399B                              418G
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GLYC_RABIT | P07511)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0070905    serine binding    Interacting selectively and non-covalently with 2-amino-3-hydroxypropanoic acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006565    L-serine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:1904482    cellular response to tetrahydrofolate    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tetrahydrofolate stimulus.
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0046655    folic acid metabolic process    The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
    GO:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GLYC_RABIT | P07511: 1cj0 1rv3 1rv4 1rvu 1rvy

(-) Related Entries Specified in the PDB File

1cj0 1CJ0 IS THE CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE
1dfo 1DFO IS THE CRYSTAL STRCUTURE OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH 5-FORMYL TETRAHYDROFOLATE AND GLYCINE
1eji 1EJI IS THE CRYSTAL STRUCTURE OF MURINE SERINE HYDROXYMETHYLTRANSFERASE TERNARY COMPLEX
1kl2 1KL2 IS THE CRYSTAL STRUCTURE OF B.STEAROTHERMOPHILUS SERINE HYDROXYMETHYLTRANSFERASE COMPLEXED WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE