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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS VAR. ALKALOPHILUS AT PH 8.5
 
Authors :  E. G. Kapetaniou, A. C. Papageorgiou
Date :  07 Sep 05  (Deposition) - 22 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Phosphoserine Aminotransferase, Pyridoxal-5'-Phosphate, Pyridine Serine Biosynthesis, Amino-Acid Biosynthesis, Aminotransferase, Pyridoxal Phosphate, Pyridoxine Biosynthesis, Serine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. G. Kapetaniou, A. Thanassoulas, A. P. Dubnovitsky, G. Nounesis, A. C. Papageorgiou
Effect Of Ph On The Structure And Stability Of Bacillus Circulans Ssp. Alkalophilus Phosphoserine Aminotransferase: Thermodynamic And Crystallographic Studies.
Proteins: Struct. , Funct. , V. 63 742 2006 Bioinf.
PubMed-ID: 16532449  |  Reference-DOI: 10.1002/PROT.20935

(-) Compounds

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
    Chains: A, B
    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
    Synonym: PSAT
    Variant: ALKALOPHILUS

 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
1PLP2Ligand/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 , ASN A:151 , THR A:153 , ASP A:173 , SER A:175 , GLN A:196 , LYS A:197 , HOH A:2220 , HOH A:2397 , ASN B:238 , THR B:239 , HOH B:2304BINDING SITE FOR RESIDUE PLP A 363
2AC2SOFTWAREASN A:238 , THR A:239 , HOH A:2280 , GLY B:76 , ALA B:77 , SER B:78 , PHE B:81 , TRP B:103 , ASN B:151 , THR B:153 , ASP B:173 , SER B:175 , GLN B:196 , LYS B:197 , HOH B:2252 , HOH B:2412BINDING SITE FOR RESIDUE PLP B 363

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C0R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:11 -Pro A:12
2Gly B:11 -Pro B:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C0R)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2C0R)

(-) 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:361
 aligned with SERC_BACCI | Q59196 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:361
                                    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 
           SERC_BACCI     2 SKRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
               SCOP domains d2c0ra_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------2c0rA01 A:17-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2c0rA02 A:259-362 Aspartate Aminotransferase, domain 1                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........hhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.eeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee.hhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c0r A   2 SERAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
                                    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 


Chain B from PDB  Type:PROTEIN  Length:361
 aligned with SERC_BACCI | Q59196 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:361
                                    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 
           SERC_BACCI     2 SKRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
               SCOP domains d2c0rb_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------2c0rB01 B:17-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2c0rB02 B:259-362 Aspartate Aminotransferase, domain 1                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........hhhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.eeeeee.hhhh.....hhhhh.....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
                 2c0r B   2 SERAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSRG 362
                                    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
   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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C0R)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 1w3u

(-) Related Entries Specified in the PDB File

1bt4 PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALKALOPHILUS
1w3u CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS VAR. ALKALOPHILUS