1JNW - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACTIVE SITE STRUCTURE OF E. COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE

Authors :   M. L. Di Salvo, T. P. Ko, F. N. Musayev, S. Raboni, V. Schirch, M. K. Safo

Date :   25 Jul 01 (Deposition) - 01 Aug 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.07

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   N-Terminal Segment, Plp, Fmn, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Di Salvo, T. P. Ko, F. N. Musayev, S. Raboni, V. Schirch, M. K. Safo
Active Site Structure And Stereospecificity Of Escherichia Coli Pyridoxine-5'-Phosphate Oxidase.
J. Mol. Biol. V. 315 385 2002
PubMed-ID: 11786019 | Reference-DOI: 10.1006/JMBI.2001.5254

Molecule 1 - PYRIDOXINE 5'-PHOSPHATE OXIDASE
	Chains	:	A
	EC Number	:	1.4.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:23 , ARG A:24 , ALA A:152 , ARG A:153 , PHE A:202 , ARG A:215 , HOH A:399 , HOH A:400 , HOH A:507	BINDING SITE FOR RESIDUE PO4 A 270
2	AC2	SOFTWARE	TYR A:17 , ARG A:67 , ILE A:68 , VAL A:69 , LEU A:70 , TYR A:82 , THR A:83 , SER A:87 , ARG A:88 , LYS A:89 , GLN A:111 , GLN A:146 , SER A:147 , TRP A:191 , ARG A:201 , PLP A:260 , HOH A:348 , HOH A:375 , HOH A:407	BINDING SITE FOR RESIDUE FMN A 250
3	AC3	SOFTWARE	ARG A:14 , TYR A:17 , LYS A:72 , TYR A:129 , ARG A:133 , ARG A:197 , HIS A:199 , PRO A:218 , FMN A:250 , HOH A:408	BINDING SITE FOR RESIDUE PLP A 260

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

(no "Cis Peptide Bond" information available for 1JNW)

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_SHIFL	188-201	1	A:188-201
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_ECOLI	188-201	1	A:188-201

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_SHIFL	188-201	2	A:188-201
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_ECOLI	188-201	2	A:188-201

(no "Exon" information available for 1JNW)

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:214
 aligned with PDXH_ECOLI | P0AFI7 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
           PDXH_ECOLI     5 DELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1jnwa_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                                SCOP domains
               CATH domains 1jnwA00 A:5-218 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------Pyridox_oxidase-1jnwA01 A:39-125                                                       ----------------------------------------------------PNPOx_C-1jnwA02 A:178-218                 Pfam domains
         Sec.struct. author ...hhhhhh.........hhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhh.........eeeeee...eeeeee.hhhhh.eeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnw A   5 DELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAmVVATVDEHGQPYQRIVLLKHYDEKGmVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVmVIGKAERLSTLEVmKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    14        24        34        44        54        64        74    |   84        94       104       114       124  |    134       144       154       164       174       184       194       204       214    
                                                                           53-MSE                    79-MSE                           113-MSE       127-MSE

Chain A from PDB  Type:PROTEIN  Length:214
 aligned with PDXH_SHIFL | P0AFI8 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
           PDXH_SHIFL     5 DELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1jnwa_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                                SCOP domains
               CATH domains 1jnwA00 A:5-218 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------Pyridox_oxidase-1jnwA01 A:39-125                                                       ----------------------------------------------------PNPOx_C-1jnwA02 A:178-218                 Pfam domains
         Sec.struct. author ...hhhhhh.........hhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhh.........eeeeee...eeeeee.hhhhh.eeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnw A   5 DELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAmVVATVDEHGQPYQRIVLLKHYDEKGmVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVmVIGKAERLSTLEVmKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    14        24        34        44        54        64        74    |   84        94       104       114       124  |    134       144       154       164       174       184       194       204       214    
                                                                           53-MSE                    79-MSE                           113-MSE       127-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: 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)

Escherichia coli [TaxId: 562] (7)

d1jnwa_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pnp Oxidase; Chain A (68)

Homologous Superfamily: Electron Transport, Fmn-binding Protein; Chain A (67)

Escherichia coli. Organism_taxid: 562. (5)

1jnwA00

A:5-218

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FMN-binding (25)

Family: Pyridox_oxidase (9)

Escherichia coli (strain K12) (2)

Pyridox_oxidase-1jnwA01

A:39-125

Clan: no clan defined [family: PNPOx_C] (4)

Family: PNPOx_C (4)

Escherichia coli (strain K12) (2)

PNPOx_C-1jnwA02

A:178-218

Asymmetric Unit(hide GO term definitions)

Chain A (PDXH_ECOLI | P0AFI7)

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:0009443	pyridoxal 5'-phosphate salvage	Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A (PDXH_SHIFL | P0AFI8)

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 Unit
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(no "Cis Peptide Bonds" information available for 1jnw)

Biological Unit
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	1jnw
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	1.4.3.5
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UniProtKB/Swiss-Prot
	PDXH_ECOLI \| P0AFI7	:	1dnl 1g76 1g77 1g78 1g79 1wv4
	PDXH_SHIFL \| P0AFI8	:	1dnl 1g76 1g77 1g78 1g79 1wv4

1dnl	1DNL IS THE ORIGINAL STRUCTURE SOLVED BY MAD WITHOUT BOUND SUBSTRATE MOLECULE
1g76	1G76 IS THE COMPLEX WITH PNP
1g77	1G77 IS THE COMPLEX WITH PLP
1g78	1G78 IS THE COMPLEX WITH 2 PLP
1g79	1G79 IS THE COMPLEX WITH 2 PLP

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

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Pfam Domains (2, 2)

Gene Ontology (10, 17)

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