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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS VAR. ALKALOPHILUS
 
Authors :  E. G. Kapetaniou, A. P. Dubnovitsky, A. C. Papageorgiou
Date :  20 Jul 04  (Deposition) - 22 Dec 04  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Phosphoserine Aminotransferase, Pyridoxal-5'-Phosphate Transferase, Pyridine Serine Biosynthesis, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Dubnovitsky, E. G. Kapetaniou, A. C. Papageorgiou
Enzyme Adaptation To Alkaline Ph: Atomic Resolution (1. 08 A) Structure Of Phosphoserine Aminotransferase From Bacillus Alcalophilus
Protein Sci. V. 14 97 2005
PubMed-ID: 15608117  |  Reference-DOI: 10.1110/PS.041029805

(-) Compounds

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
    Atcc: 21783
    Chains: A
    EC Number: 2.6.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397
    Other Details: SCHIFF BASE LINK BETWEEN A 197 AND A 363
    Synonym: PHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE, PSAT
    Variant: ALKALOPHILUS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:76 , ALA A:77 , SER A:78 , PHE A:81 , TRP A:103 , THR A:153 , ASP A:173 , SER A:175 , GLN A:196 , LYS A:197 , ASN A:238 , THR A:239 , HOH A:2238 , HOH A:2336 , HOH A:2337BINDING SITE FOR RESIDUE PLP A1363
2AC2SOFTWARELEU A:113 , HIS A:220 , LEU A:221 , PRO A:222 , ARG A:359 , HOH A:2222 , HOH A:2338 , HOH A:2339 , HOH A:2340BINDING SITE FOR RESIDUE GOL A1364

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W3U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W3U)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_BACCI188-207  1A:188-207
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_BACCI188-207  2A:188-207

(-) Exons   (0, 0)

(no "Exon" information available for 1W3U)

(-) 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:360
 aligned with SERC_BACCI | Q59196 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_BACCI     3 KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
               SCOP domains d1w3ua_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------1w3uA01 A:17-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              1w3uA02 A:259-362 Aspartate Aminotransferase, domain 1                                                   CATH domains
               Pfam domains --Aminotran_5-1w3uA01 A:5-350                                                                                                                                                                                                                                                                                                                               ------------ Pfam domains
         Sec.struct. author ...ee........hhhhhhhhhhhh.hhhhh..hhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhheeeeeee.hhhh...............eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee.hhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w3u A   3 ERAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
                                    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
   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, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (SERC_BACCI | Q59196)
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.
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

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

UniProtKB/Swiss-Prot
        SERC_BACCI | Q59196: 1bt4 2c0r

(-) Related Entries Specified in the PDB File

1bt4 PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALKALOPHILUS