2A2J - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXINE 5'-PHOSPHATE OXIDASE (RV2607) FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   J. -D. Pedelacq, B. -S. Rho, C. -Y. Kim, G. S. Waldo, T. P. Lekin, B. W. Sege B. Rupp, L. -W. Hung, S. -I. Kim, T. C. Terwilliger, Mycobacterium Tub Structural Proteomics Project (Xmtb)

Date :   22 Jun 05 (Deposition) - 23 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Barrel, Structural Genomics, Mycobacterium Tuberculosis Structural Proteomics Project, Xmtb, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -D. Pedelacq, B. -S. Rho, C. -Y. Kim, G. S. Waldo, T. P. Lekin, B. W. Segelke, B. Rupp, L. -W. Hung, S. -I. Kim, T. C. Terwilliger
Crystal Structure Of A Putative Pyridoxine 5'-Phosphate Oxidase (Rv2607) From Mycobacterium Tuberculosis.
Proteins V. 62 563 2005
PubMed-ID: 16374842 | Reference-DOI: 10.1002/PROT.20824

Molecule 1 - PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
	Chains	:	A, B
	EC Number	:	1.4.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B DERIVATIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	PNP/PMP OXIDASE, PNPOX

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE

(no "Site" information available for 2A2J)

(no "SS Bond" information available for 2A2J)

(no "Cis Peptide Bond" information available for 2A2J)

(no "SAP(SNP)/Variant" information available for 2A2J)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_MYCTO	198-211	2	A:198-211 B:198-211
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_MYCTU	198-211	2	A:198-211 B:198-211

(no "Exon" information available for 2A2J)

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:203
 aligned with PDXH_MYCTO | P9WIJ0 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:203
                                                                                                                                                                                                                                  224  
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|  
           PDXH_MYCTO    24 PEKDGCGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQP--   -
               SCOP domains d2a2ja1 A:24-224 Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                            -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeeeeeeee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..........eeeeee...eeeeee.......eeeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS--------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2j A  24 PEKDGcGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQPGS 226
                                 |  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                 |                                                                                                                                                                                                     
                                29-CME

Chain A from PDB  Type:PROTEIN  Length:203
 aligned with PDXH_MYCTU | P9WIJ1 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:203
                                                                                                                                                                                                                                  224  
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|  
           PDXH_MYCTU    24 PEKDGCGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQP--   -
               SCOP domains d2a2ja1 A:24-224 Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                            -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeeeeeeee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..........eeeeee...eeeeee.......eeeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS--------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2j A  24 PEKDGcGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQPGS 226
                                 |  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                29-CME

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with PDXH_MYCTO | P9WIJ0 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:203
                                                                                                                                                                                                                                  224  
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|  
           PDXH_MYCTO    24 PEKDGCGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQP--   -
               SCOP domains d2a2jb_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....hhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh...........eeeeee...eeeeee.......eeeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS--------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2j B  24 PEKDGcGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQPGS 226
                                 |  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                29-CME

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with PDXH_MYCTU | P9WIJ1 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:203
                                                                                                                                                                                                                                  224  
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|  
           PDXH_MYCTU    24 PEKDGCGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQP--   -
               SCOP domains d2a2jb_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....hhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh...........eeeeee...eeeeee.......eeeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS--------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2j B  24 PEKDGcGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQPGS 226
                                 |  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                29-CME

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/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Split barrel-like (99)

Superfamily: FMN-binding split barrel (90)

Family: PNP-oxidase like (53)

Protein domain: Pyridoxine 5'-phoshate oxidase (PNP oxidase) (16)

Mycobacterium tuberculosis [TaxId: 1773] (1)

1a	d2a2ja1	A:24-224
1b	d2a2jb_	B:

(no "CATH Domain" information available for 2A2J)

(no "Pfam Domain" information available for 2A2J)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXH_MYCTO | P9WIJ0)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0004733	pyridoxamine-phosphate oxidase activity	Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	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.
	GO:0042816	vitamin B6 metabolic process	The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

Chain A,B (PDXH_MYCTU | P9WIJ1)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0004733	pyridoxamine-phosphate oxidase activity	Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	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.
	GO:0042816	vitamin B6 metabolic process	The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

Asymmetric/Biological Unit
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