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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A SERINE HYDROXYMETHYL TRANSFERASE IN APO FORM FROM BURKHOLDERIA CENOCEPACIA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  18 Sep 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Serine Hydroxymethyl Transferase, Transferase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Fairman, M. M. Jensen, A. H. Sullivan, J. Abendroth, T. E. Edwards D. Lorimer
X-Ray Crystal Structure Of A Serine Hydroxymethyl Transferase In Apo Form From Burkholderia Cenocepacia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLYA, GLYA1, BCEJ2315_31420, BCAL3197
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Strain: J2315
    Synonym: SHMT, SERINE METHYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:99 , SER A:100 , THR A:227 , HIS A:229 , LYS A:230 , HOH A:748 , HOH A:858 , GLY B:260 , GLY B:261 , HOH B:886BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWARESER A:137 , LYS A:139 , HOH A:669 , HOH A:765 , HOH A:883 , SER B:252 , ALA B:253 , ILE B:254 , PHE B:255 , ILE B:258 , HOH B:686BINDING SITE FOR RESIDUE PO4 A 502
3AC3SOFTWAREPRO B:42 , THR B:369 , ARG B:370 , VAL B:413 , TYR B:414 , HOH B:729 , HOH B:751 , HOH B:829BINDING SITE FOR RESIDUE EDO B 501
4AC4SOFTWAREGLY A:260 , GLY A:261 , HOH A:636 , SER B:98 , GLY B:99 , SER B:100 , THR B:227 , HIS B:229 , LYS B:230 , HOH B:674 , HOH B:711 , HOH B:961BINDING SITE FOR RESIDUE PO4 B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:132 -Pro A:133
2Phe B:255 -Pro B:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MSO)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4msoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeeee............eeeeee..hhhhhhhhhhhhh..eeeehhhhhhh..hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee.hhhhh....eeeee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeee.hhhh.hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mso A   2 FDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLGSPVNMSGKWFNVVSYGLIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    11        21        31        41        51    ||  75        85        95       105       115      |133       143    || 158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308|      322       332       342       352       362       372       382       392       402       412   
                                                                                 56|                                                122|              148|                                                                                                                                                       308|                                                                                                      
                                                                                  71                                                 131               154                                                                                                                                                        313                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4msob_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..hhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeeee......eeeeee...hhhhhhhhhhhhh..eeeehhhhhhh..hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee.hhhhh....eeeee...hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee......eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mso B   2 FDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQLTNKYYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLSGKWFNVVSYGLDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVDMAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPINSAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLVKRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVRAQVAELTKRFPVYR 415
                                    11        21        31        41        51    ||  75        85        95       105       115      |139       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413  
                                                                                 56|                                                122|        148|                                                                                                                                                                                                                                                                      
                                                                                  71                                                 137         153
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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