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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE L-LACTATE OXIDASE
 
Authors :  Y. Morimoto
Date :  19 Jul 06  (Deposition) - 05 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Fmn, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Umena, K. Yorita, T. Matsuoka, A. Kita, K. Fukui, Y. Morimoto
The Crystal Structure Of L-Lactate Oxidase From Aerococcus Viridans At 2. 1A Resolution Reveals The Mechanism Of Strict Substrate Recognition
Biochem. Biophys. Res. Commun. V. 350 249 2006
PubMed-ID: 17007814  |  Reference-DOI: 10.1016/J.BBRC.2006.09.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTATE OXIDASE
    Chains: A, B, C, D
    EC Number: 1.13.12.4
    Organism Scientific: AEROCOCCUS VIRIDANS
    Organism Taxid: 1377

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FMN4Ligand/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:5001 , HOH A:5015 , HOH A:5123 , HOH A:5624 , HOH A:5716BINDING SITE FOR RESIDUE FMN A 512
2AC2SOFTWAREALA B:1092 , PRO B:1093 , ILE B:1094 , ALA B:1095 , SER B:1122 , GLN B:1144 , TYR B:1146 , THR B:1172 , LYS B:1241 , SER B:1263 , HIS B:1265 , GLY B:1266 , ARG B:1268 , ASP B:1296 , SER B:1297 , GLY B:1298 , ARG B:1300 , GLY B:1319 , ARG B:1320 , HOH B:5003 , HOH B:5030 , HOH B:5074BINDING SITE FOR RESIDUE FMN B 1512
3AC3SOFTWAREALA C:2092 , PRO C:2093 , ILE C:2094 , ALA C:2095 , SER C:2122 , GLN C:2144 , TYR C:2146 , THR C:2172 , LYS C:2241 , SER C:2263 , HIS C:2265 , GLY C:2266 , ARG C:2268 , ASP C:2296 , SER C:2297 , GLY C:2298 , ARG C:2300 , GLY C:2319 , ARG C:2320 , HOH C:5016 , HOH C:5018 , HOH C:5060BINDING SITE FOR RESIDUE FMN C 2512
4AC4SOFTWAREALA D:3092 , PRO D:3093 , ILE D:3094 , ALA D:3095 , SER D:3122 , GLN D:3144 , TYR D:3146 , THR D:3172 , LYS D:3241 , SER D:3263 , HIS D:3265 , GLY D:3266 , ARG D:3268 , ASP D:3296 , SER D:3297 , GLY D:3298 , ARG D:3300 , GLY D:3319 , ARG D:3320 , HOH D:5013 , HOH D:5090 , HOH D:5143BINDING SITE FOR RESIDUE FMN D 3512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DU2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DU2)

(-) Exons   (0, 0)

(no "Exon" information available for 2DU2)

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

    Alignment length:374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
        Q44467_9LACT      1 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY  374
               SCOP domains d2du2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhh...............hhhhh...............hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2du2 A    1 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY  374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    


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

    Alignment length:374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
        Q44467_9LACT      1 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY  374
               SCOP domains d2du2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...ee...............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhh.........hhhhh.......hhhhhh.......hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2du2 B 1001 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 1374
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370    


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

    Alignment length:374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
        Q44467_9LACT      1 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY  374
               SCOP domains d2du2c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...ee...............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhheeeeeee........hhhhhhhh.........hhhhhh......hhhhhhhhh....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2du2 C 2001 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 2374
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320      2330      2340      2350      2360      2370    


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

    Alignment length:374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
        Q44467_9LACT      1 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY  374
               SCOP domains d2du2d_ D: 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.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhh.........hhhhh.......hhhhhhhhh....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2du2 D 3001 MNNNDIEYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 3374
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240      3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360      3370
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DU2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DU2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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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  2du2
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  Q44467_9LACT | Q44467
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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: 2e77 2j6x 2nli 2zfa 4rje 4yl2 5ebu

(-) Related Entries Specified in the PDB File

1gox GLYCOLATE OXIDASE