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(-) Description

Title :  STRUCTURE OF LACTATE OXIDASE AT PH4.5 FROM AEROCOCCUS VIRIDANS
 
Authors :  M. Furuichi, D. Balasundaresan, N. Suzuki, Y. Yoshida, H. Minagawa, H. Kaneko, I. Waga, P. K. R. Kumar, H. Mizuno
Date :  26 Dec 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  A  (4x)
Biol. Unit 3:  B  (4x)
Keywords :  L-Lactate Oxidase, Flavoenzyme, Fmn, D-Lactate, Oxidoreductase, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Furuichi, N. Suzuki, B. Dhakshnamoorhty, H. Minagawa, R. Yamagishi, Y. Watanabe, Y. Goto, H. Kaneko, Y. Yoshida, H. Yagi, I. Waga, P. K. R. Kumar, H. Mizuno
X-Ray Structures Of Aerococcus Viridans Lactate Oxidase And Its Complex With D-Lactate At Ph 4. 5 Show An Alpha-Hydroxyacid Oxidation Mechanism
J. Mol. Biol. V. 378 436 2008
PubMed-ID: 18367206  |  Reference-DOI: 10.1016/J.JMB.2008.02.062
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTATE OXIDASE
    Chains: A, B
    EC Number: 1.13.12.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROCOCCUS VIRIDANS
    Organism Taxid: 1377

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB
Biological Unit 2 (4x): A 
Biological Unit 3 (4x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FMN8Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , ALA A:92 , PRO A:93 , ILE A:94 , ALA A:95 , SER A:122 , GLN A:144 , TYR A:146 , THR A:172 , LYS A:241 , SER A:263 , HIS A:265 , GLY A:266 , ARG A:268 , ASP A:296 , SER A:297 , GLY A:298 , ARG A:300 , GLY A:319 , ARG A:320 , HOH A:386 , HOH A:406 , HOH A:430BINDING SITE FOR RESIDUE FMN A 375
2AC2SOFTWARETYR A:146 , ASP A:174 , THR A:176 , HIS A:265 , GLN A:269 , HOH A:492BINDING SITE FOR RESIDUE EDO A 376
3AC3SOFTWAREILE B:41 , ALA B:92 , PRO B:93 , ILE B:94 , ALA B:95 , SER B:122 , GLN B:144 , TYR B:146 , THR B:172 , LYS B:241 , SER B:263 , HIS B:265 , GLY B:266 , ARG B:268 , ASP B:296 , SER B:297 , GLY B:298 , ARG B:300 , GLY B:319 , ARG B:320 , HOH B:400 , HOH B:478 , HOH B:483BINDING SITE FOR RESIDUE FMN B 375
4AC4SOFTWARETYR B:146 , THR B:172 , ASP B:174 , THR B:176 , HIS B:265 , GLN B:269 , HOH B:540BINDING SITE FOR RESIDUE EDO B 376

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZFA)

(-) 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:352
 aligned with Q44467_9LACT | Q44467 from UniProtKB/TrEMBL  Length:374

    Alignment length:367
                                    17        27        37        47        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       
         Q44467_9LACT     8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
               SCOP domains d2zfaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh...hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee......hhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh....eeee............--------..hhhhhhhhh....-------........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee............hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfa A   8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRD--------FGMPIVQRYLRGTAE-------YGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      |  -     | 197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       
                                                                                                                                                                                                          184      193           207     215                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:329
 aligned with Q44467_9LACT | Q44467 from UniProtKB/TrEMBL  Length:374

    Alignment length:368
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
         Q44467_9LACT     7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
               SCOP domains d2zfab_ B: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------FMN_dh-2zfaB01 B:29-367                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) ----------------------FMN_dh-2zfaB02 B:29-367                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eee......hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....eeee.....---------------------------------------......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee............hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfa B   7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTV---------------------------------------ASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176|        -         -         -         -|      226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
                                                                                                                                                                                                    177                                     217
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q44467_9LACT | Q44467)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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  1.13.12.4
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 Related Entries

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

UniProtKB/TrEMBL
        Q44467_9LACT | Q44467: 2du2 2e77 2j6x 2nli 4rje 4yl2 5ebu

(-) Related Entries Specified in the PDB File

2nli CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN L-LACTATE OXIDASE AND A SUBSTRATE ANALOGUE AT 1.59 ANGSTROM RESOLUTION