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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYL TRANSFERASE FROM BURKHOLDERIA CENOCEPACIA BOUND TO PLP AND GLYCINE
 
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 Glycine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLYA, BCAL3197
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Strain: J2315
    Synonym: SHMT, 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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GLY4Mod. Amino AcidGLYCINE
3PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GLY2Mod. Amino AcidGLYCINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GLY2Mod. Amino AcidGLYCINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:98 , GLY A:99 , SER A:100 , HIS A:127 , SER A:176 , ASP A:201 , ALA A:203 , HIS A:204 , THR A:227 , HIS A:229 , LYS A:230 , GLY A:501 , TYR C:56 , GLY C:260 , GLY C:261 , HOH C:839BINDING SITE FOR RESIDUE PLP A 500
2AC2SOFTWARESER A:36 , HIS A:127 , HIS A:204 , LYS A:230 , ARG A:361 , PLP A:500 , TYR C:66BINDING SITE FOR RESIDUE GLY A 501
3AC3SOFTWARESER B:98 , GLY B:99 , SER B:100 , HIS B:127 , ALA B:175 , SER B:176 , ASP B:201 , HIS B:204 , THR B:227 , HIS B:229 , LYS B:230 , GLY B:502 , HOH B:649 , TYR D:56 , GLY D:260 , GLY D:261 , HOH D:928 , HOH D:964BINDING SITE FOR RESIDUE PLP B 501
4AC4SOFTWARESER B:36 , HIS B:204 , LYS B:230 , ARG B:361 , PLP B:501 , TYR D:56 , TYR D:66BINDING SITE FOR RESIDUE GLY B 502
5AC5SOFTWAREALA B:109 , MET B:110 , TYR B:197BINDING SITE FOR RESIDUE EDO B 503
6AC6SOFTWARETYR A:56 , GLY A:260 , GLY A:261 , HOH A:641 , HOH A:684 , 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 , GLY C:701 , HOH C:840BINDING SITE FOR RESIDUE PLP C 700
7AC7SOFTWARETYR A:56 , TYR A:66 , HOH A:674 , SER C:36 , HIS C:127 , HIS C:204 , LYS C:230 , ARG C:361 , PLP C:700BINDING SITE FOR RESIDUE GLY C 701
8AC8SOFTWARETYR B:56 , GLY B:260 , GLY B:261 , 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 , GLY D:801 , HOH D:954 , HOH D:955BINDING SITE FOR RESIDUE PLP D 800
9AC9SOFTWARETYR B:56 , TYR B:66 , SER D:36 , HIS D:204 , LYS D:230 , ARG D:361 , PLP D:800BINDING SITE FOR RESIDUE GLY D 801

(-) SS Bonds  (0, 0)

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

(-) 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 4OTL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OTL)

(-) 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:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhh....eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4otl A   7 STIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    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         


Chain B from PDB  Type:PROTEIN  Length:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhh....eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4otl B   7 STIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    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         


Chain C 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..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee.hhhhh....eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4otl C   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 D from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.hhhhh....eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4otl D   0 HMFDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNENEDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                     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
   Legend:   → Mismatch (orange background)
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  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 4OTL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/TrEMBL
        B4ECY9_BURCJ | B4ECY9: 4mso 4n0w 4ot8

(-) Related Entries Specified in the PDB File

4mso
4n0w
4ot8 RELATED ID: SSGCID-BUCEA.00008.A RELATED DB: TARGETTRACK