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(-) Description

Title :  PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ FROM CAMPYLOBACTER JEJUNI
 
Authors :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  28 Jul 10  (Deposition) - 11 Aug 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Idp90671, Center For Structural Genomics Of Infectious Diseases, Csgid, Pyridoxine Synthesis, Vitamin B6, Pyridoxal Phosphate, Pdxj, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
Pyridoxal Phosphate Biosynthetic Protein Pdxj From Campylobacter Jejuni.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXINE 5'-PHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.6.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CJ1238, PDXJ
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: PNP SYNTHASE

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , GLY A:209 , HIS A:210 , GLY A:211 , ILE A:231 , GLY A:232 , GLN A:233 , HOH A:275 , HOH A:313 , HOH A:333 , HOH A:354 , HOH A:423BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREHIS A:9 , ARG A:17 , ARG A:47 , HIS A:48 , HOH A:267 , HOH A:277 , HOH A:359 , HOH A:386 , HOH A:549BINDING SITE FOR RESIDUE PO4 A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O6C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:21 -Pro A:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O6C)

(-) Exons   (0, 0)

(no "Exon" information available for 3O6C)

(-) 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:259
 aligned with PDXJ_CAMJE | Q9PN59 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:259
                              1                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248         
           PDXJ_CAMJE     - --MLLGVNIDHIAVLRQARMVNDPDLLEAAFIVARHGDQITLHVREDRRHAQDFDLENIIKFCKSPVNLECALNDEILNLALKLKPHRVTLVPEKREELTTEGGLCLNHAKLKQSIEKLQNANIEVSLFINPSLEDIEKSKILKAQFIELHTGHYANLHNALFSNISHTAFALKELDQDKKTLQAQFEKELQNLELCAKKGLELGLKVAAGHGLNYKNVKPVVKIKEICELNIGQSIVARSVFTGLQNAILEMKELIKR 257
               SCOP domains d3o6ca_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --PdxJ-3o6cA01 A:1-257                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhh....hhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...hhhhh...........hhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee........hhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o6c A  -1 NAmLLGVNIDHIAVLRQARmVNDPDLLEAAFIVARHGDQITLHVREDRRHAQDFDLENIIKFCKSPVNLECALNDEILNLALKLKPHRVTLVPEKREELTTEGGLCLNHAKLKQSIEKLQNANIEVSLFINPSLEDIEKSKILKAQFIELHTGHYANLHNALFSNISHTAFALKELDQDKKTLQAQFEKELQNLELCAKKGLELGLKVAAGHGLNYKNVKPVVKIKEICELNIGQSIVARSVFTGLQNAILEmKELIKR 257
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  |      
                              |               18-MSE                                                                                                                                                                                                                                  251-MSE  
                              1-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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O6C)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDXJ_CAMJE | Q9PN59)
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:0033856    pyridoxine 5'-phosphate synthase activity    Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H(2)O + H(+) + phosphate + pyridoxine 5'-phosphate.
    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.
    GO:0016769    transferase activity, transferring nitrogenous groups    Catalysis of the transfer of a nitrogenous group from one compound (donor) to another (acceptor).
biological process
    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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 Related Entries

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        PDXJ_CAMJE | Q9PN59: 3o6d

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3o6d