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(-) Description

Title :  2.25 ANGSTROM CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE (SERC) FROM SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
 
Authors :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papa W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  03 Feb 11  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson
2. 25 Angstrom Crystal Structure Of Phosphoserine Aminotransferase (Serc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
    ChainsA, B
    EC Number2.6.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21
    Expression System Taxid526563
    Expression System Vector TypePLASMID
    GeneSERC, STM0977
    Organism ScientificSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid90371
    StrainLT2
    SynonymPHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE, PSAT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:280 , SER A:283 , TYR A:286 , HOH A:467 , HOH A:468BINDING SITE FOR RESIDUE CA A 363
2AC2SOFTWAREILE B:280 , SER B:283 , TYR B:286 , HOH B:458 , HOH B:459BINDING SITE FOR RESIDUE CA B 363

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QM2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:10 -Pro A:11
2Gln A:24 -Glu A:25
3Gly B:10 -Pro B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QM2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_SALTY189-208
 
  2A:189-208
B:189-208

(-) Exons   (0, 0)

(no "Exon" information available for 3QM2)

(-) 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:330
 aligned with SERC_SALTY | P55900 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:360
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           SERC_SALTY     3 QVFNFSSGPAMLPAEVLKLAQQELCDWHGLGTSVMEISHRGKEFIQVAEEAEQDFRDLLNIPSNYKVLFCHGGGRGQFAGVPLNLLGDKTTADYVDAGYWAASAIKEAKKYCAPQIIDAKITVDGKRAVKPMREWQLSDNAAYLHYCPNETIDGIAIDETPDFGPEVVVTADFSSTILSAPLDVSRYGVIYAGAQKNIGPAGLTLVIVREDLLGKAHESCPSILDYTVLNDNDSMFNTPPTFAWYLSGLVFKWLKAQGGVAAMHKINQQKAELLYGVIDNSDFYRNDVAQANRSRMNVPFQLADNTLDKVFLEESFAAGLHALKGHRVVGGMRASIYNAMPIEGVKALTDFMIDFERRHG 362
               SCOP domains d3qm2a_ A: automated ma                       tches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee........hhhhhhhhh..-----------------------.hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeeeee.eeee..eeee.hhhhh........eee..ee....ee............eeee..........hhhhh.eeeee.........eeeeeee.hhh.......hhhhhhhhhhhh-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeeee.hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qm2 A   3 QVFNFSSGPAMLPAEVLKLAQQE-----------------------VAEEAEQDFRDLLNIPSNYKVLFCHGGGRGQFAGVPLNLLGDKTTADYVDAGYWAASAIKEAKKYCAPQIIDAKITVDGKRAVKPMREWQLSDNAAYLHYCPNETIDGIAIDETPDFGPEVVVTADFSSTILSAPLDVSRYGVIYAGAQKNIGPAGLTLVIVREDLLGKAHESCPSILDYTVLNDN-------PTFAWYLSGLVFKWLKAQGGVAAMHKINQQKAELLYGVIDNSDFYRNDVAQANRSRMNVPFQLADNTLDKVFLEESFAAGLHALKGHRVVGGMRASIYNAMPIEGVKALTDFMIDFERRHG 362
                                    12        22  |      -         -      | 52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 |     242       252       262       272       282       292       302       312       322       332       342       352       362
                                                 25                      49                                                                                                                                                                                      234     242                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:331
 aligned with SERC_SALTY | P55900 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:360
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           SERC_SALTY     3 QVFNFSSGPAMLPAEVLKLAQQELCDWHGLGTSVMEISHRGKEFIQVAEEAEQDFRDLLNIPSNYKVLFCHGGGRGQFAGVPLNLLGDKTTADYVDAGYWAASAIKEAKKYCAPQIIDAKITVDGKRAVKPMREWQLSDNAAYLHYCPNETIDGIAIDETPDFGPEVVVTADFSSTILSAPLDVSRYGVIYAGAQKNIGPAGLTLVIVREDLLGKAHESCPSILDYTVLNDNDSMFNTPPTFAWYLSGLVFKWLKAQGGVAAMHKINQQKAELLYGVIDNSDFYRNDVAQANRSRMNVPFQLADNTLDKVFLEESFAAGLHALKGHRVVGGMRASIYNAMPIEGVKALTDFMIDFERRHG 362
               SCOP domains d3qm2b_ B: automated mat                      ches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -Aminotran_5-3qm2B01 B:4                      -350                                                                                                                                                                                                                                                                                                          ------------ Pfam domains (1)
           Pfam domains (2) -Aminotran_5-3qm2B02 B:4                      -350                                                                                                                                                                                                                                                                                                          ------------ Pfam domains (2)
         Sec.struct. author ..ee........hhhhhhhhhhh.----------------------..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeeeee.eeee..eeee.hhhhh........eee..ee....ee............eeee..........hhhhh.eeeee.........eeeeeee.hhh.......hhhhhhhhhh..-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...hhhhh...eeeeee.hhhhhhhhhhhhhh..ee..........eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qm2 B   3 QVFNFSSGPAMLPAEVLKLAQQEL----------------------VAEEAEQDFRDLLNIPSNYKVLFCHGGGRGQFAGVPLNLLGDKTTADYVDAGYWAASAIKEAKKYCAPQIIDAKITVDGKRAVKPMREWQLSDNAAYLHYCPNETIDGIAIDETPDFGPEVVVTADFSSTILSAPLDVSRYGVIYAGAQKNIGPAGLTLVIVREDLLGKAHESCPSILDYTVLNDN-------PTFAWYLSGLVFKWLKAQGGVAAMHKINQQKAELLYGVIDNSDFYRNDVAQANRSRMNVPFQLADNTLDKVFLEESFAAGLHALKGHRVVGGMRASIYNAMPIEGVKALTDFMIDFERRHG 362
                                    12        22   |     -         -      | 52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 |     242       252       262       272       282       292       302       312       322       332       342       352       362
                                                  26                     49                                                                                                                                                                                      234     242                                                                                                                        

   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  (0, 0)

(no "CATH Domain" information available for 3QM2)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SERC_SALTY | P55900)
molecular function
    GO:0004648    O-phospho-L-serine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.
    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: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:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of 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:0008615    pyridoxine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
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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