1G77 - JenaLib

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Title :   X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5`-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION

Authors :   M. K. Safo, F. N. Musayev, M. L. Di Salvo, V. Schirch

Date :   09 Nov 00 (Deposition) - 29 Nov 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Plp Complex, Fmn Complex, Pyridoxine 5'-Phosphate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Safo, F. N. Musayev, M. L. Di Salvo, V. Schirch
X-Ray Structure Of Escherichia Coli Pyridoxine 5'-Phosphate Oxidase Complexed With Pyridoxal 5'-Phosphate At 2. 0 A Resolution.
J. Mol. Biol. V. 310 817 2001
PubMed-ID: 11453690 | Reference-DOI: 10.1006/JMBI.2001.4734

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, 8)

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	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 16)

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	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:23 , ARG A:24 , ARG A:120 , ALA A:152 , ARG A:153 , ARG A:215 , HOH A:310 , HOH A:329 , HOH A:336	BINDING SITE FOR RESIDUE PO4 A 280
2	AC2	SOFTWARE	SER A:148 , ARG A:149	BINDING SITE FOR RESIDUE PO4 A 290
3	AC3	SOFTWARE	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:308 , HOH A:312 , HOH A:322	BINDING SITE FOR RESIDUE FMN A 250
4	AC4	SOFTWARE	LYS A:72 , TYR A:129 , ARG A:133 , GLN A:146 , ARG A:197 , HIS A:199 , PRO A:218 , FMN A:250 , HOH A:338	BINDING SITE FOR RESIDUE PLP A 260

(no "SS Bond" information available for 1G77)

(no "Cis Peptide Bond" information available for 1G77)

(no "SAP(SNP)/Variant" information available for 1G77)

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 1G77)

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:199
 aligned with PDXH_ECOLI | P0AFI7 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:199
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
           PDXH_ECOLI    20 GGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1g77a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                 SCOP domains
               CATH domains 1g77A00 A:20-218 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeeeeeeee..eeeeeee..hhhhhhhhhh.eeeeee..hhh.eeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhh............eeeeeeeeeeeeeee.hhhhh.eeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g77 A  20 GGLRRRDLPADPLTLFERWLSQACEAKLADPTAmVVATVDEHGQPYQRIVLLKHYDEKGmVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVmVIGKAERLSTLEVmKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    29        39        49   |    59        69        79        89        99       109   |   119       129       139       149       159       169       179       189       199       209         
                                                            53-MSE                    79-MSE                           113-MSE       127-MSE

Chain A from PDB  Type:PROTEIN  Length:199
 aligned with PDXH_SHIFL | P0AFI8 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:199
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
           PDXH_SHIFL    20 GGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1g77a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                 SCOP domains
               CATH domains 1g77A00 A:20-218 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeeeeeeee..eeeeeee..hhhhhhhhhh.eeeeee..hhh.eeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhh............eeeeeeeeeeeeeee.hhhhh.eeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g77 A  20 GGLRRRDLPADPLTLFERWLSQACEAKLADPTAmVVATVDEHGQPYQRIVLLKHYDEKGmVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVmVIGKAERLSTLEVmKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    29        39        49   |    59        69        79        89        99       109   |   119       129       139       149       159       169       179       189       199       209         
                                                            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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

d1g77a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

1g77A00

A:20-218

(no "Pfam Domain" information available for 1G77)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1g77)

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

1g76	1G76 CONTAINS THE SAME PROTEIN COMPLEXED WITH THE SAME LIGAND. HOWEVER, THE NUMBER OF BOUND LIGANDS DIFFER.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (4, 4)

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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Gene Ontology (10, 17)

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