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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE OXIDASE FROM AEROCOCCUS VIRIDANS CONTAINING FAD
 
Authors :  E. C. M. Juan, M. T. Hossain, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Takenaka
Date :  03 Apr 06  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. M. 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE OXIDASE
    Chains: A
    EC Number: 1.2.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AEROCOCCUS VIRIDANS
    Organism Taxid: 1377

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO416Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:119 , ASN A:120 , HIS A:127 , ARG A:133 , HOH A:1745 , HOH A:1750 , HOH A:2031 , HOH A:2179BINDING SITE FOR RESIDUE SO4 A 1603
2AC2SOFTWAREVAL A:335 , GLU A:336 , GLU A:337BINDING SITE FOR RESIDUE SO4 A 1604
3AC3SOFTWAREARG A:209 , LEU A:586 , GLU A:587 , HOH A:1775 , HOH A:1981 , HOH A:2047BINDING SITE FOR RESIDUE SO4 A 1605
4AC4SOFTWAREGLY A:390 , MET A:417 , GLY A:441 , ASP A:442 , GLY A:443 , ALA A:444 , TYR A:472 , HOH A:1657 , HOH A:1774 , HOH A:1791 , HOH A:1857 , HOH A:2040BINDING SITE FOR RESIDUE SO4 A 1606
5AC5SOFTWAREPHE 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 , PRO A:283 , PHE A:284 , ASP A:301 , ILE A:302 , ASP A:303 , MET A:306 , GLY A:319 , ASP A:320 , ALA A:321 , VAL A:389 , SER A:411 , PRO A:412 , ALA A:415 , HOH A:1691 , HOH A:1692 , HOH A:1723 , HOH A:1858 , HOH A:1871 , HOH A:1877 , HOH A:2220BINDING SITE FOR RESIDUE FAD A 1601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DJI)

(-) Exons   (0, 0)

(no "Exon" information available for 2DJI)

(-) Sequences/Alignments

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:590
 aligned with A9X9K8_9LACT | A9X9K8 from UniProtKB/TrEMBL  Length:592

    Alignment length:590
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
         A9X9K8_9LACT     3 DNKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKHEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAILGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAIAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYEPIAPAAQDIDAAVELLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEALTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDIDPAMLGKRHHADVAILGDAGLAIDEILNKVDAVEESAWWTANLKNIANWREYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLDSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK 592
               SCOP domains d2djia2 A:3-186 Pyruvate oxidase                                                                                                                                                        d2djia1 A:187-363 Pyruvate oxidase                                                                                                                                               d2djia3 A:364-592 Pyruvate oxidase                                                                                                                                                                                                    SCOP domains
               CATH domains 2djiA01 A:3-185  [code=3.40.50.970, no name defined]                                                                                                                                   ----2djiA02 A:190-354 TPP-binding domain                                                                                                                                 2djiA03 A:355-544  [code=3.40.50.970, no name defined]                                                                                                                                        ------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhh.........eeee..hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.........hhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.eee.hhh..hhhhh........hhhhhhhhhhhhhh...eeeee.hhhh.hhhhhhhhhhhhh..eee...hhhhh...............hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee....hhhhhhhhhhh...........hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhh......hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dji A   3 DNKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKHEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAILGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAIAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYAPIAPAAQDIDAAVELLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEALTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDIDPAMLGKRHHADVAILGDAALAIDEILNKVDAVEESAWWTANLKNIANWREYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLDSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK 592
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (A9X9K8_9LACT | A9X9K8)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0047112    pyruvate oxidase activity    Catalysis of the reaction: H(+) + O(2) + phosphate + pyruvate = acetyl phosphate + CO(2) + H(2)O(2).
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A9X9K8_9LACT | A9X9K8: 1v5e

(-) Related Entries Specified in the PDB File

1pox THE SAME PROTEIN FROM LACTOBACILLUS PLANTARUM
1v5e THE SAME PROTEIN AND SOURCE. ALSO CONTAINS THE FAD COFACTOR
1v5f THE SAME PROTEIN AND SOURCE. CONTAINS THDP AND MAGNESIUM IN ADDITION TO FAD
1v5g THE SAME PROTEIN AND SOURCE. CONTAINS ACTHDP AND MAGNESIUM IN ADDITION TO FAD