3EY9 - JenaLib

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Title :   STRUCTURAL BASIS FOR MEMBRANE BINDING AND CATALYTIC ACTIVATION OF THE PERIPHERAL MEMBRANE ENZYME PYRUVATE OXIDASE FROM ESCHERICHIA COLI

Authors :   P. Neumann, A. Weidner, A. Pech, M. T. Stubbs, K. Tittmann

Date :   20 Oct 08 (Deposition) - 04 Nov 08 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Pyruvate Oxidase, Membrane-Associated Flavoprotein Dehydrogenase, Interactions With Lipids, Cell Membrane, Fad, Flavoprotein, Lipid- Binding, Magnesium, Membrane, Oxidoreductase, Thiamine Pyrophosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Neumann, A. Weidner, A. Pech, M. T. Stubbs, K. Tittmann
Structural Basis For Membrane Binding And Catalytic Activation Of The Peripheral Membrane Enzyme Pyruvate Oxidase From Escherichia Coli.
Proc. Natl. Acad. Sci. Usa V. 105 17390 2008
PubMed-ID: 18988747 | Reference-DOI: 10.1073/PNAS.0805027105

Molecule 1 - PYRUVATE DEHYDROGENASE [CYTOCHROME]
	Chains	:	A, B
	EC Number	:	1.2.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PYYC102
	Expression System Strain	:	ZK126
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	POXB, B0871, JW0855
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PYRUVATE OXIDASE, POX, PYRUVATE DEHYDROGENASE, ALPHA- PEPTIDE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION
4	TDP	2	Ligand/Ion	THIAMIN DIPHOSPHATE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION
4	TDP	4	Ligand/Ion	THIAMIN DIPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:381 , THR A:382 , PRO A:383 , GLY A:406 , MET A:408 , GLY A:432 , ASP A:433 , GLY A:434 , GLY A:435 , ASN A:460 , VAL A:462 , LEU A:463 , GLY A:464 , MG A:616 , THR B:25 , GLU B:50 , SER B:73 , HIS B:80 , GLN B:113 , SO4 B:621	BINDING SITE FOR RESIDUE TDP A 611
2	AC2	SOFTWARE	HIS A:92 , GLY A:209 , SER A:210 , GLY A:211 , ALA A:233 , LEU A:234 , ARG A:235 , GLY A:236 , THR A:251 , GLY A:252 , LEU A:253 , ILE A:254 , GLY A:273 , THR A:274 , GLN A:275 , PHE A:276 , PRO A:277 , TYR A:278 , ASP A:292 , ILE A:293 , ASN A:294 , SER A:297 , GLY A:310 , ASP A:311 , ILE A:312 , PHE A:403 , ASN A:404 , TYR A:549 , PHE B:112	BINDING SITE FOR RESIDUE FAD A 612
3	AC3	SOFTWARE	GLY A:26 , ASP A:27 , SER A:28 , CYS A:74 , GLN A:113 , TDP B:611	BINDING SITE FOR RESIDUE SO4 A 621
4	AC4	SOFTWARE	ASP A:433 , PHE A:458 , ASN A:460 , VAL A:462 , TDP A:611	BINDING SITE FOR RESIDUE MG A 616
5	AC5	SOFTWARE	THR A:25 , GLU A:50 , SER A:73 , HIS A:80 , GLN A:113 , SO4 A:621 , GLY B:381 , THR B:382 , PRO B:383 , GLY B:406 , MET B:408 , GLY B:432 , ASP B:433 , GLY B:434 , GLY B:435 , ASN B:460 , VAL B:462 , LEU B:463 , GLY B:464 , MG B:617	BINDING SITE FOR RESIDUE TDP B 611
6	AC6	SOFTWARE	PHE A:112 , HIS B:92 , GLY B:209 , SER B:210 , GLY B:211 , ALA B:233 , LEU B:234 , ARG B:235 , GLY B:236 , THR B:251 , GLY B:252 , LEU B:253 , ILE B:254 , GLY B:273 , THR B:274 , GLN B:275 , PHE B:276 , TYR B:278 , ASP B:292 , ILE B:293 , ASN B:294 , SER B:297 , GLY B:310 , ASP B:311 , ILE B:312 , PHE B:403 , ASN B:404 , TYR B:549	BINDING SITE FOR RESIDUE FAD B 612
7	AC7	SOFTWARE	ASP B:433 , PHE B:458 , ASN B:460 , VAL B:462 , TDP B:611	BINDING SITE FOR RESIDUE MG B 617
8	AC8	SOFTWARE	TDP A:611 , GLY B:26 , ASP B:27 , SER B:28 , SER B:73 , CYS B:74 , GLN B:113	BINDING SITE FOR RESIDUE SO4 B 621

(no "SS Bond" information available for 3EY9)

(no "Cis Peptide Bond" information available for 3EY9)

(no "SAP(SNP)/Variant" information available for 3EY9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	POXB_ECOLI	416-435	2	A:416-435 B:416-435

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	POXB_ECOLI	416-435	4	A:416-435 B:416-435

(no "Exon" information available for 3EY9)

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:571
 aligned with POXB_ECOLI | P07003 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:571
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571 
           POXB_ECOLI     2 KQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAHSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKLEQAKGFSLYMLRAIISGRGDEVIELAKTNWLR 572
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhh........hhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhh....................hhhhhhhhhhhhhh...eeeee.hhhh.hhhhhhhhhhhhh..eee...hhhhhh.....eeee.....hhhhhhhhhh..eeeee.....hhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhh..hhhhhhhh....eeeeee..........................hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh...hhhhh.eee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ey9 A   2 KQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAHSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKLEQAKGFSLYMLRAIISGRGDEVIELAKTNWLR 572
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571

Chain B from PDB  Type:PROTEIN  Length:571
 aligned with POXB_ECOLI | P07003 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:571
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571 
           POXB_ECOLI     2 KQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAHSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKLEQAKGFSLYMLRAIISGRGDEVIELAKTNWLR 572
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhh........hhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhh....................hhhhhhhhhhhhhh...eeeee.hhhh.hhhhhhhhhhhhh..eee...hhhhhh.....eeee.....hhhhhhhhhh..eeeee.....hhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee..........................hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh...hhhhh.eee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ey9 B   2 KQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAHSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKLEQAKGFSLYMLRAIISGRGDEVIELAKTNWLR 572
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571

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 '\|'

(no "SCOP Domain" information available for 3EY9)

(no "CATH Domain" information available for 3EY9)

(no "Pfam Domain" information available for 3EY9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (POXB_ECOLI | P07003)

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:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0052737	pyruvate dehydrogenase (quinone) activity	Catalysis of the reaction: a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2.
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0042867	pyruvate catabolic process	The chemical reactions and pathways resulting in the breakdown of pyruvate, 2-oxopropanoate.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	POXB_ECOLI \| P07003	:	3eya

1pow	PYRUVATE OXIDASE FROM LACTOBACILLUS PLANTARUM
3eya

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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