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(-) Description

Title :  THE STRUCTURE OF L-AMINO ACID OXIDASE FROM RHODOCOCCUS OPACUS IN COMPLEX WITH O-AMINOBENZOATE
 
Authors :  A. Faust, K. Niefind, W. Hummel, D. Schomburg
Date :  01 Dec 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Amino Acid Oxidase, Hydride Transfer Mechanism, Gr2- Family, Flavoenzyme, Fad Containing, Oxidoreductase, Inhibitor Complex, Dimerisation Mode (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Faust, K. Niefind, W. Hummel, D. Schomburg
The Structure Of A Bacterial L-Amino Acid Oxidase From Rhodococcus Opacus Gives New Evidence For The Hydride Mechanism For Dehydrogenation
J. Mol. Biol. V. 367 234 2007
PubMed-ID: 17234209  |  Reference-DOI: 10.1016/J.JMB.2006.11.071
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-AMINO ACID OXIDASE
    Atcc: 51882
    Chains: A, B
    EC Number: 1.4.3.2
    Fragment: RESIDUES 46-534
    Organism Scientific: RHODOCOCCUS OPACUS
    Organism Taxid: 37919
    Other Details: DSM 43250

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BE22Ligand/Ion2-AMINOBENZOIC ACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLY A:21 , PRO A:22 , ALA A:23 , LEU A:41 , GLU A:42 , ALA A:43 , ARG A:44 , GLY A:48 , GLY A:49 , ARG A:50 , VAL A:51 , GLY A:81 , ALA A:82 , THR A:83 , ARG A:84 , ALA A:259 , VAL A:261 , SER A:321 , TYR A:371 , TRP A:416 , TYR A:421 , ALA A:425 , GLY A:458 , ASP A:459 , ALA A:466 , TRP A:467 , GLN A:468 , ALA A:471 , BE2 A:1490 , HOH A:2037 , HOH A:2098 , HOH A:2324 , HOH A:2478 , HOH A:2479 , HOH A:2480BINDING SITE FOR RESIDUE FAD A1489
2AC2SOFTWAREARG A:84 , GLN A:228 , TYR A:371 , ALA A:466 , TRP A:467 , FAD A:1489 , HOH A:2481BINDING SITE FOR RESIDUE BE2 A1490
3AC3SOFTWAREGLY B:19 , GLY B:21 , PRO B:22 , ALA B:23 , LEU B:41 , GLU B:42 , ALA B:43 , ARG B:44 , GLY B:49 , ARG B:50 , ALA B:82 , THR B:83 , ARG B:84 , ALA B:259 , VAL B:261 , THR B:292 , ILE B:293 , SER B:321 , TYR B:371 , TRP B:416 , TYR B:421 , ALA B:425 , GLY B:458 , ASP B:459 , ALA B:466 , TRP B:467 , GLN B:468 , ALA B:471 , BE2 B:1490 , HOH B:2041 , HOH B:2111 , HOH B:2500 , HOH B:2501 , HOH B:2502 , HOH B:2503 , HOH B:2504BINDING SITE FOR RESIDUE FAD B1489
4AC4SOFTWAREARG B:84 , GLN B:228 , TYR B:371 , ALA B:466 , TRP B:467 , FAD B:1489 , HOH B:2504BINDING SITE FOR RESIDUE BE2 B1490

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JB3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:230 -Met A:231
2Met B:230 -Met B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JB3)

(-) Exons   (0, 0)

(no "Exon" information available for 2JB3)

(-) Sequences/Alignments

Asymmetric/Biological 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:479
 aligned with Q8VPD4_RHOOP | Q8VPD4 from UniProtKB/TrEMBL  Length:534

    Alignment length:486
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527      
         Q8VPD4_RHOOP    48 DLIGKVKGSHSVVVLGGGPAGLCSAFELQKAGYKVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCRELGVEIQGFGNQNANTFVNYQSDTSLSGQSVTYRAAKADTFGYMSELLKKATDQGALDQVLSREDKDALSEFLSDFGDLSDDGRYLGSSRRGYDSEPGAGLNFGTEKKPFAMQEVIRSGIGRNFSFDFGYDQAMMMFTPVGGMDRIYYAFQDRIGTDNIVFGAEVTSMKNVSEGVTVEYTAGGSKKSITADYAICTIPPHLVGRLQNNLPGDVLTALKAAKPSSSGKLGIEYSRRWWETEDRIYGGASNTDKDISQIMFPYDHYNSDRGVVVAYYSSGKRQEAFESLTHRQRLAKAIAEGSEIHGEKYTRDISSSFSGSWRRTKYSESAWANWAGSGGSHGGAATPEYEKLLEPVDKIYFAGDHLSNAIAWQHGALTSARDVVTHIHERVAQE 533
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee..hhhhhhhhhhhhhh..eeeee...........eee...eee.....eee.......eee.....ee..hhhhhhhhhhh..eeee.......eee...........eehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..........hhhh.eee.........ee....hhhhhhhhh...hhhhhhh......eeee....hhhhhhhhhhhh...ee...eeeeeeee..eeeeeeee..eeeeeee.eeee..hhhhhh..ee..hhhhhhhhhhee...eeeeeeee..hhhhhh......eeee.....eee..........eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhh........ee...-------.hhhhhhhh.....eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jb3 A   4 DLIGKVKGSHSVVVLGGGPAGLCSAFELQKAGYKVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCRELGVEIQGFGNQNANTFVNYQSDTSLSGQSVTYRAAKADTFGYMSELLKKATDQGALDQVLSREDKDALSEFLSDFGDLSDDGRYLGSSRRGYDSEPGAGLNFGTEKKPFAMQEVIRSGIGRNFSFDFGYDQAMMMFTPVGGMDRIYYAFQDRIGTDNIVFGAEVTSMKNVSEGVTVEYTAGGSKKSITADYAICTIPPHLVGRLQNNLPGDVLTALKAAKPSSSGKLGIEYSRRWWETEDRIYGGASNTDKDISQIMFPYDHYNSDRGVVVAYYSSGKRQEAFESLTHRQRLAKAIAEGSEIHGEKYTRDISSSFSGSWRRTKYSESAWANWAGS-------ATPEYEKLLEPVDKIYFAGDHLSNAIAWQHGALTSARDVVTHIHERVAQE 489
                                    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        |-      |443       453       463       473       483      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      432     440                                                 


Chain B from PDB  Type:PROTEIN  Length:477
 aligned with Q8VPD4_RHOOP | Q8VPD4 from UniProtKB/TrEMBL  Length:534

    Alignment length:485
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527     
         Q8VPD4_RHOOP    48 DLIGKVKGSHSVVVLGGGPAGLCSAFELQKAGYKVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCRELGVEIQGFGNQNANTFVNYQSDTSLSGQSVTYRAAKADTFGYMSELLKKATDQGALDQVLSREDKDALSEFLSDFGDLSDDGRYLGSSRRGYDSEPGAGLNFGTEKKPFAMQEVIRSGIGRNFSFDFGYDQAMMMFTPVGGMDRIYYAFQDRIGTDNIVFGAEVTSMKNVSEGVTVEYTAGGSKKSITADYAICTIPPHLVGRLQNNLPGDVLTALKAAKPSSSGKLGIEYSRRWWETEDRIYGGASNTDKDISQIMFPYDHYNSDRGVVVAYYSSGKRQEAFESLTHRQRLAKAIAEGSEIHGEKYTRDISSSFSGSWRRTKYSESAWANWAGSGGSHGGAATPEYEKLLEPVDKIYFAGDHLSNAIAWQHGALTSARDVVTHIHERVAQ 532
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------Amino_oxidase-2jb3B01 B:22-483                                                                                                                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) ------------------Amino_oxidase-2jb3B02 B:22-483                                                                                                                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ..........eeeee..hhhhhhhhhhhhhh..eeeee...........eee...eee.....eee.......eee.....ee..hhhhhhhhhhh..eeee.......eee...........eehhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.........hhhh.eee.........ee....hhhhhhhhh...hhhhhhh......eeee....hhhhhhhhhhhh...ee..eeeeeeeee..eeeeeeee..eeeeeee.eeee..hhhhhh..ee..hhhhhhhhh.ee...eeeeeeee..hhhhhh......eeee.....eee..........eeeeeeeeehhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhh.eeeeeeee.hhh........ee..--------.hhhhhhh......eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb3 B   4 DLIGKVKGSHSVVVLGGGPAGLCSAFELQKAGYKVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCRELGVEIQGFGNQNANTFVNYQSDTSLSGQSVTYRAAKADTFGYMSELLKKATDQGALDQVLSREDKDALSEFLSDFGDLSDDGRYLGSSRRGYDSEPGAGLNFGTEKKPFAMQEVIRSGIGRNFSFDFGYDQAMMMFTPVGGMDRIYYAFQDRIGTDNIVFGAEVTSMKNVSEGVTVEYTAGGSKKSITADYAICTIPPHLVGRLQNNLPGDVLTALKAAKPSSSGKLGIEYSRRWWETEDRIYGGASNTDKDISQIMFPYDHYNSDRGVVVAYYSSGKRQEAFESLTHRQRLAKAIAEGSEIHGEKYTRDISSSFSGSWRRTKYSESAWANWAG--------ATPEYEKLLEPVDKIYFAGDHLSNAIAWQHGALTSARDVVTHIHERVAQ 488
                                    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       | -      |443       453       463       473       483     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     431      440
   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  (0, 0)

(no "SCOP Domain" information available for 2JB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JB3)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8VPD4_RHOOP | Q8VPD4)
molecular function
    GO:0001716    L-amino-acid oxidase activity    Catalysis of the reaction: a L-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide.
    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.
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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  1.4.3.2
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 Related Entries

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

UniProtKB/TrEMBL
        Q8VPD4_RHOOP | Q8VPD4: 2jae 2jb1 2jb2

(-) Related Entries Specified in the PDB File

2jae THE STRUCTURE OF L-AMINO ACID OXIDASE FROM RHODOCOCCUS OPACUS IN THE UNBOUND STATE
2jb1 THE L-AMINO ACID OXIDASE FROM RHODOCOCCUS OPACUS IN COMPLEX WITH L-ALANINE
2jb2 THE STRUCTURE OF L-AMINO ACID OXIDASE FROM RHODOCOCCUS OPACUS IN COMPLEX WITH L- PHENYLALANINE.