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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE IN TERNARY COMPLEX WITH DUMP AND TOMUDEX
 
Authors :  A. Dowiercial, A. Jarmula, W. R. Rypniewski, P. Wilk, W. Rode
Date :  23 Mar 12  (Deposition) - 02 May 12  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Ternary Complex, Methyltransferase, Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dowiercial, P. Wilk, W. Rypniewski, W. Rode, A. Jarmula
Crystal Structure Of Mouse Thymidylate Synthase In Tertiary Complex With Dump And Raltitrexed Reveals N-Terminus Architecture And Two Different Active Site Conformations.
Biomed Res Int V. 2014 45803 2014
PubMed-ID: 24995339  |  Reference-DOI: 10.1155/2014/945803

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPIGDM4
    Expression System Strain: TX61-
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TYMS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric Unit (6, 21)
No.NameCountTypeFull Name
1D164Ligand/IonTOMUDEX
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL10Ligand/IonGLYCEROL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5SO41Ligand/IonSULFATE ION
6UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (6, 14)
No.NameCountTypeFull Name
1D162Ligand/IonTOMUDEX
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL7Ligand/IonGLYCEROL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5SO41Ligand/IonSULFATE ION
6UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1D162Ligand/IonTOMUDEX
2DTT-1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL3Ligand/IonGLYCEROL
4MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5SO4-1Ligand/IonSULFATE ION
6UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 3 (6, 14)
No.NameCountTypeFull Name
1D162Ligand/IonTOMUDEX
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3GOL7Ligand/IonGLYCEROL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5SO41Ligand/IonSULFATE ION
6UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:44 , CYS A:189 , HIS A:190 , GLN A:208 , ARG A:209 , SER A:210 , GLY A:211 , ASP A:212 , ASN A:220 , HIS A:250 , TYR A:252 , D16 A:402 , HOH A:502 , HOH A:625 , ARG B:169 , ARG B:170BINDING SITE FOR RESIDUE UMP A 401
02AC2SOFTWAREPHE A:74 , ILE A:102 , TRP A:103 , ASP A:212 , LEU A:215 , GLY A:216 , PHE A:219 , ASN A:220 , TYR A:252 , LYS A:302 , MET A:303 , MET A:305 , ALA A:306 , UMP A:401 , HOH A:517 , HOH A:635 , HOH A:665 , HOH A:684 , HOH A:746 , HOH A:855 , HOH A:893BINDING SITE FOR RESIDUE D16 A 402
03AC3SOFTWAREGLN A:154 , LYS A:157 , VAL A:158 , THR A:161 , ASP A:168 , ARG A:170 , ILE A:172 , HOH A:550 , HOH A:562 , HOH A:631 , HOH A:793 , LEU B:181BINDING SITE FOR RESIDUE DTT A 403
04AC4SOFTWAREASP A:167 , VAL A:198 , ASN A:199 , HOH A:645 , HOH A:767 , LYS B:40 , LYS B:41 , GLU B:42BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREASN A:177 , LYS A:179 , HOH A:702 , HOH A:853 , GLY B:137 , ASN B:177 , LYS B:179BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREHOH A:618 , HOH A:628BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREARG A:277 , LYS A:278 , HOH A:797 , LYS B:87 , LYS B:98BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWAREARG A:268 , PRO A:297 , HIS A:298 , PRO A:299BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREARG A:169 , ARG A:170 , ARG B:44 , CYS B:189 , HIS B:190 , GLN B:208 , ARG B:209 , SER B:210 , ASP B:212 , ASN B:220 , HIS B:250 , TYR B:252 , D16 B:402 , HOH B:595 , HOH B:838BINDING SITE FOR RESIDUE UMP B 401
10BC1SOFTWAREPHE B:74 , ILE B:102 , TRP B:103 , ASN B:106 , ASP B:212 , LEU B:215 , GLY B:216 , PHE B:219 , TYR B:252 , LYS B:302 , MET B:303 , MET B:305 , ALA B:306 , UMP B:401 , HOH B:570 , HOH B:612 , HOH B:679 , HOH B:680 , HOH B:715 , HOH B:774 , HOH B:832BINDING SITE FOR RESIDUE D16 B 402
11BC2SOFTWARELEU B:115 , LEU B:181 , PRO B:182 , MET B:184 , PRO B:187 , HOH B:512 , HOH B:532 , HOH B:738 , HOH B:796 , HOH B:846BINDING SITE FOR RESIDUE GOL B 403
12BC3SOFTWARELYS A:40 , LYS A:41 , GLU A:42 , HOH A:741 , ASP B:167 , VAL B:198 , ASN B:199 , HOH B:740BINDING SITE FOR RESIDUE GOL B 404
13BC4SOFTWAREHIS B:22 , GLU B:24 , LEU B:25 , PRO B:269 , HOH B:566BINDING SITE FOR RESIDUE GOL B 405
14BC5SOFTWAREARG B:36 , CYS B:37 , GLY B:38 , PHE B:39 , LYS B:40 , HOH B:843BINDING SITE FOR RESIDUE MES B 406
15BC6SOFTWAREARG C:44 , CYS C:189 , HIS C:190 , ARG C:209 , SER C:210 , ASP C:212 , GLY C:216 , ASN C:220 , HIS C:250 , TYR C:252 , D16 C:402 , HOH C:505 , HOH C:694 , ARG D:169 , ARG D:170BINDING SITE FOR RESIDUE UMP C 401
16BC7SOFTWAREPHE C:74 , ARG C:101 , ASP C:212 , LEU C:215 , GLY C:216 , PHE C:219 , TYR C:252 , UMP C:401 , HOH C:564 , HOH C:618 , HOH C:622 , HOH C:680 , HOH C:741BINDING SITE FOR RESIDUE D16 C 402
17BC8SOFTWAREARG C:21 , ARG C:58 , HOH C:606 , HOH C:754BINDING SITE FOR RESIDUE GOL C 403
18BC9SOFTWAREARG C:169 , ARG C:170 , ARG D:44 , CYS D:189 , HIS D:190 , ARG D:209 , SER D:210 , GLY D:211 , ASP D:212 , GLY D:216 , ASN D:220 , HIS D:250 , TYR D:252 , D16 D:402 , HOH D:566BINDING SITE FOR RESIDUE UMP D 401
19CC1SOFTWAREPHE D:74 , ILE D:102 , ASP D:212 , LEU D:215 , GLY D:216 , PHE D:219 , TYR D:252 , LYS D:302 , MET D:303 , UMP D:401 , HOH D:603 , HOH D:686 , HOH D:699BINDING SITE FOR RESIDUE D16 D 402
20CC2SOFTWAREARG D:36 , CYS D:37 , GLY D:38 , PHE D:39 , GOL D:404BINDING SITE FOR RESIDUE GOL D 403
21CC3SOFTWAREASN C:199 , PHE D:39 , LYS D:40 , GOL D:403BINDING SITE FOR RESIDUE GOL D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EB4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EB4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EB4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EB4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EB4)

(-) Sequences/Alignments

Asymmetric 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4eb4a_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eb4 A   1 MLVVGSELQSDAQRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKMEMAV 307
                                    10  ||    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
                                       13|                                                                                                                                                                                                                                                                                              
                                        21                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4eb4b_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb4 B   1 MLVVGSELQSDAQPRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKMEMAV 307
                                    10  ||    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 
                                       13|                                                                                                                                                                                                                                                                                               
                                        20                                                                                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4eb4c_ C: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb4 C   1 MLVVGSELQSDAQRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIK 302
                                    10  ||    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297     
                                       13|                                                                                                                                                                                                                                                                                         
                                        21                                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4eb4d_ D: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb4 D   1 MLVVGSELQSDAQRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKME 304
                                    10  ||    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       
                                       13|                                                                                                                                                                                                                                                                                           
                                        21
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EB4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EB4)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        TYSY_MOUSE | P07607: 3ihi 4e5o 4ein 4ez8 5fct

(-) Related Entries Specified in the PDB File

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