1V5G - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE BETWEEN PYRUVATE OXIDASE CONTAINING FAD AND TPP, AND SUBSTRATE PYRUVATE

Authors :   M. T. Hossain, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Take

Date :   22 Nov 03 (Deposition) - 28 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Oxidoreductase, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. C. Juan, M. M. Hoque, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, T. Sekiguchi, A. Takenaka
The Structures Of Pyruvate Oxidase From Aerococcus Viridans With Cofactors And With A Reaction Intermediate Reveal The Flexibility Of The Active-Site Tunnel For Catalysis.
Acta Crystallogr. , Sect. F V. 63 900 2007
PubMed-ID: 18007037 | Reference-DOI: 10.1107/S1744309107041012

Molecule 1 - PYRUVATE OXIDASE
	Chains	:	A
	EC Number	:	1.2.3.3
	Organism Scientific	:	AEROCOCCUS VIRIDANS
	Organism Taxid	:	1377

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	HTL	1	Ligand/Ion	2-ACETYL-THIAMINE DIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	HTL	4	Ligand/Ion	2-ACETYL-THIAMINE DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:442 , ASN A:469 , GLU A:471 , HTL A:1602 , HOH A:1604	BINDING SITE FOR RESIDUE MG A 1603
2	AC2	SOFTWARE	PHE A:116 , GLY A:215 , ILE A:216 , GLY A:217 , THR A:239 , GLY A:240 , LYS A:241 , THR A:257 , TYR A:258 , ARG A:259 , VAL A:260 , GLY A:279 , SER A:280 , ASN A:281 , PHE A:282 , PHE A:284 , ASP A:301 , ILE A:302 , ASP A:303 , MET A:306 , GLY A:319 , ASP A:320 , ALA A:321 , SER A:411 , PRO A:412 , ALA A:415 , HTL A:1602 , HOH A:1657 , HOH A:1714 , HOH A:1733 , HOH A:1792 , HOH A:1855 , HOH A:1969	BINDING SITE FOR RESIDUE FAD A 1601
3	AC3	SOFTWARE	PRO A:28 , GLU A:54 , SER A:77 , PRO A:80 , HIS A:84 , GLN A:117 , VAL A:389 , ASN A:391 , ALA A:415 , MET A:417 , GLY A:441 , ASP A:442 , GLY A:443 , ALA A:444 , ASN A:469 , GLU A:471 , TYR A:472 , ALA A:473 , PHE A:474 , ILE A:475 , FAD A:1601 , MG A:1603 , HOH A:1604 , HOH A:1605 , HOH A:1618	BINDING SITE FOR RESIDUE HTL A 1602

(no "SS Bond" information available for 1V5G)

(no "Cis Peptide Bond" information available for 1V5G)

(no "SAP(SNP)/Variant" information available for 1V5G)

(no "PROSITE Motif" information available for 1V5G)

(no "Exon" information available for 1V5G)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:589
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d1v5ga2 A:4-177 automated matches                                                                                                                                             d1v5ga1 A:178-360 automated matches                                                                                                                                                    d1v5ga3 A:361-592 automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 1v5gA01 A:4-185  [code=3.40.50.970, no name defined]                                                                                                                                  ----1v5gA02 A:190-354 TPP-binding domain                                                                                                                                 1v5gA03 A:355-544  [code=3.40.50.970, no name defined]                                                                                                                                        ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.........hhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh.eee.hhh..hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhh...eee...hhhhh......eee......hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...........hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhh......hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5g A   4 NKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKHEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAILGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAIAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYAPIAPAAQDIDAAVELLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEALTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDIDPAMLGKRHHADVAILGDAALAIDEILNKVDAVEESAWWTANLKNIANWREYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLDSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK 592
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.970, no name defined] (144)

Aerococcus viridans. Organism_taxid: 1377 (3)

1a	1v5gA03	A:355-544
1b	1v5gA01	A:4-185

Homologous Superfamily: TPP-binding domain (120)

Aerococcus viridans. Organism_taxid: 1377 (3)

1v5gA02

A:190-354

(no "Pfam Domain" information available for 1V5G)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1V5G)

Asymmetric Unit
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		Biological Unit 1	[ Jena3D ]

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1pox	THE SAME PROTEIN FROM LACTOBACILLUS PLANTARUM
1v5e	PYRUVATE OXIDASE CONTAINING FAD
1v5f	PYRUVATE OXIDASE COMPLEXED WITH FAD AND TPP

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