3O6D - JenaLib

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Title :   PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ FROM CAMPYLOBACTER JEJUNI IN COMPLEX WITH PYRIDOXINE-5'-PHOSPHATE

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 :   1.95

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, Pyridoxine-5'-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of Pyridoxal Phosphate Biosynthetic Protein Pdxj From Campylobacter Jejuni.
To Be Published
PubMed: search

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	PXP	1	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	4	Ligand/Ion	PHOSPHATE ION
3	PXP	2	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:6 , ARG A:17 , GLU A:68 , PHE A:127 , GLU A:147 , HIS A:210 , GLY A:211 , ASN A:230 , ILE A:231 , GLY A:232 , GLN A:233 , HOH A:258 , HOH A:263 , HOH A:270 , PO4 A:802	BINDING SITE FOR RESIDUE PXP A 801
2	AC2	SOFTWARE	ASP A:8 , HIS A:9 , ARG A:17 , HIS A:48 , HOH A:258 , HOH A:287 , HOH A:320 , HOH A:328 , PXP A:801	BINDING SITE FOR RESIDUE PO4 A 802
3	AC3	SOFTWARE	ASN A:155	BINDING SITE FOR RESIDUE PO4 A 803

(no "SS Bond" information available for 3O6D)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3O6D)

(no "PROSITE Motif" information available for 3O6D)

(no "Exon" information available for 3O6D)

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
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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 d3o6da_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --PdxJ-3o6dA01 A:1-257                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhh....hhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...hhhhh...........hhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o6d 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Pyridoxine 5'-phosphate synthase (11)

Family: automated matches (3)

Protein domain: automated matches (3)

Campylobacter jejuni [TaxId: 192222] (2)

d3o6da_

(no "CATH Domain" information available for 3O6D)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: PdxJ (3)

Campylobacter jejuni (2)

PdxJ-3o6dA01

A:1-257

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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	Cis Peptide Bonds
		Asp A:21 - Pro A:22	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2.6.99.2
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	PDXJ_CAMJE \| Q9PN59	:	3o6c

3o6c	PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ FROM CAMPYLOBACTER JEJUNI. RELATED ID: IDP90671 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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