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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYL TRANSFERASE FROM BURKHOLDERIA CENOCEPACIA BOUND TO PLP AND SERINE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  13 Feb 14  (Deposition) - 23 Apr 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Serine Hydroxymethyl Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Fairman, M. M. Jensen, A. H. Sullivan, T. E. Edwards, D. Lorimer
X-Ray Crystal Structure Of Serine Hydroxymethyl Transferase From Burkholderia Cenocepacia Bound To Plp And Serine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.1.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGLYA, BCAL3197
    Organism ScientificBURKHOLDERIA CENOCEPACIA
    Organism Taxid216591
    StrainJ2315
    SynonymSHMT, SERINE METHYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SER4Mod. Amino AcidSERINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SER2Mod. Amino AcidSERINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SER2Mod. Amino AcidSERINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:98 , GLY A:99 , SER A:100 , HIS A:127 , SER A:176 , ASP A:201 , HIS A:204 , THR A:227 , HIS A:229 , LYS A:230 , SER A:502 , HOH A:763 , TYR C:56 , GLY C:260 , GLY C:261 , HOH C:804BINDING SITE FOR RESIDUE PLP A 501
2AC2SOFTWARESER A:36 , HIS A:127 , HIS A:204 , LYS A:230 , ARG A:361 , PLP A:501 , TYR C:56 , GLU C:58 , TYR C:66BINDING SITE FOR RESIDUE SER A 502
3AC3SOFTWARETYR A:56 , GLU A:58 , TYR A:66 , SER C:36 , HIS C:127 , HIS C:204 , LYS C:230 , ARG C:361 , PLP C:700BINDING SITE FOR RESIDUE SER A 503
4AC4SOFTWARESER B:98 , GLY B:99 , SER B:100 , HIS B:127 , SER B:176 , ASP B:201 , ALA B:203 , HIS B:204 , THR B:227 , HIS B:229 , LYS B:230 , SER B:502 , HOH B:760 , TYR D:56 , GLY D:260 , GLY D:261 , HOH D:938 , HOH D:1004BINDING SITE FOR RESIDUE PLP B 501
5AC5SOFTWARESER B:36 , HIS B:127 , SER B:176 , HIS B:204 , LYS B:230 , ARG B:361 , PLP B:501 , GLU D:58 , TYR D:66BINDING SITE FOR RESIDUE SER B 502
6AC6SOFTWARETYR B:56 , GLU B:58 , TYR B:66 , SER D:36 , HIS D:127 , HIS D:204 , ARG D:361 , PLP D:800BINDING SITE FOR RESIDUE SER B 503
7AC7SOFTWARETYR A:56 , GLY A:260 , GLY A:261 , SER A:503 , HOH A:642 , SER C:98 , GLY C:99 , SER C:100 , HIS C:127 , ALA C:175 , SER C:176 , ASP C:201 , ALA C:203 , HIS C:204 , THR C:227 , HIS C:229 , LYS C:230 , HOH C:894BINDING SITE FOR RESIDUE PLP C 700
8AC8SOFTWARETYR B:56 , GLY B:260 , GLY B:261 , SER B:503 , HOH B:672 , SER D:98 , GLY D:99 , SER D:100 , HIS D:127 , ALA D:175 , SER D:176 , ASP D:201 , HIS D:204 , THR D:227 , HIS D:229 , LYS D:230 , HOH D:1002BINDING SITE FOR RESIDUE PLP D 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OT8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:255 -Pro A:256
2Phe B:255 -Pro B:256
3Phe C:255 -Pro C:256
4Phe D:255 -Pro D:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OT8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OT8)

(-) Exons   (0, 0)

(no "Exon" information available for 4OT8)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhh.eeeee........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ot8 A   2 FDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    

Chain B from PDB  Type:PROTEIN  Length:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhh.eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ot8 B   5 AQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    14        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 

Chain C from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhh.eeeee........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ot8 C   0 HMFDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409     

Chain D from PDB  Type:PROTEIN  Length:408
                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhh.eeeee........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ot8 D   7 STIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVY 414
                                    16        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        

   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  (0, 0)

(no "SCOP Domain" information available for 4OT8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OT8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OT8)

(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/TrEMBL
        B4ECY9_BURCJ | B4ECY94mso 4n0w 4otl

(-) Related Entries Specified in the PDB File

4mso
4n0w RELATED ID: SSGCID-BUCEA.00008.A RELATED DB: TARGETTRACK
4otl