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(-) Description

Title :  SERINE HYDROXYMETHYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. Osipiuk, B. Nocek, M. Zhou, J. Stam, W. F. Anderson, A. Joachimiak, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  20 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Idp01011, Serine Hydroxymethyltransferase, Salmonella Typhimurium. , One-Carbon Metabolism, Pyridoxal Phosphate, Transferase, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Osipiuk, B. Nocek, M. Zhou, J. Stam, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of Serine Hydroxymethyltransferase From Salmonella Typhimurium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG19C
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGLYA, STM2555
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602
    StrainLT2
    SynonymSERINE METHYLASE, SHMT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric/Biological Unit (2, 27)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:196 , GLU B:247 , LYS B:251BINDING SITE FOR RESIDUE ACT B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GBX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GBX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GBX)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYA_SALTY221-237
 
  2A:221-237
B:221-237

(-) Exons   (0, 0)

(no "Exon" information available for 3GBX)

(-) 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:390
 aligned with GLYA_SALTY | P0A2E1 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:420
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                
                               |     7        17        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       317       327       337       347       357       367       377       387       397       407       417
           GLYA_SALTY     - ---MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMNLAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA 417
               SCOP domains d3gbxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------3gbxA01 A:40-279               Type I PLP-dependent aspartate aminotransferase-like             (Major domain)                                                                                                                                  -3gbxA02 A:281-417 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh..--------------hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeeeee.------------hhhhhheeeeeee......hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee.hhhhh....eeeee...hhhhhhhhhhhh.----...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gbx A  -2 SNAmLKREmNIADYDAELWQAmEQEKVRQEEHIELIASENYTSPRVmQAQGSQLTNKYA--------------VDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGmNLA------------FSGKLYNIVPYGIDESGKIDYDEmAKLAKEHKPKmIIGGFSAYSGVVDWAKmREIADSIGAYLFVDmAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGDEELYKKLNSAVF----GGPLmHVIAGKAVALKEAmEPEFKVYQQQVAKNAKAmVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWmCDVLDNINDEATIERVKAKVLDICARFPVYA 417
                               |    |7        17 |      27        37      | 47        |-         -   |    77        87        97       107       117 |  |    -       137       147       157|      167 |     177       187       197   |   207       217       227       237       247       257    |  267       277  |    287       297|      307       317       327       337       347       357       367       377       387       397       407       417
                               |    |           19-MSE                   44-MSE      56             71                                             119-MSE         135                    158-MSE    169-MSE          186-MSE        201-MSE                                                 257  262   |           280-MSE           298-MSE                                                                                 386-MSE                           
                               1-MSE|                                                                                                                 122                                                                                                                                             266-MSE                                                                                                                                                   
                                    6-MSE                                                                                                                                                                                                                                                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:383
 aligned with GLYA_SALTY | P0A2E1 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:420
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                
                               |     7        17        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       317       327       337       347       357       367       377       387       397       407       417
           GLYA_SALTY     - ---MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMNLAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA 417
               SCOP domains d3gbxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------3gbxB01 B:40-279                 Type I PLP-dependent aspartate aminotransferase-                  like (Major domain)                                                                                                                          -3gbxB02 B:281-417 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh.----------------hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeeee------------------..eeeeee.......hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhhhh..---...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhh..ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gbx B  -2 SNAmLKREmNIADYDAELWQAmEQEKVRQEEHIELIASENYTSPRVmQAQGSQLTNKY----------------DVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGmN------------------LYNIVPYGIDESGKIDYDEmAKLAKEHKPKmIIGGFSAYSGVVDWAKmREIADSIGAYLFVDmAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGDEELYKKLNSAVFP---GGPLmHVIAGKAVALKEAmEPEFKVYQQQVAKNAKAmVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWmCDVLDNINDEATIERVKAKVLDICARFPVYA 417
                               |    |7        17 |      27        37      | 47       | -         -    |   77        87        97       107       117 ||      -         - |     147       157|      167 |     177       187       197   |   207       217       227       237       247       257|   |  267       277  |    287       297|      307       317       327       337       347       357       367       377       387       397       407       417
                               1-MSE|           19-MSE                   44-MSE     55               72                                            119-MSE             139                158-MSE    169-MSE          186-MSE        201-MSE                                                  258 262   |           280-MSE           298-MSE                                                                                 386-MSE                           
                                    6-MSE                                                                                                           120                                                                                                                                               266-MSE                                                                                                                                                   

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GBX)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLYA_SALTY | P0A2E1)
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: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: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: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:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    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:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

1dfo CRYSTAL STRUCTURE AT 2.4 A RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE SUBSTRATE AND 5-FORMYL TETRAHYDROFOLATE. RELATED ID: IDP01011 RELATED DB: TARGETDB