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(-) Description

Title :  CRYSTAL STRUCTURE OF ACYL COA DEHYDROGENASE
 
Authors :  T. Hikima, Y. Kawano, Y. Nodake, N. Kamiya, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  11 May 07  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acyl-Coa Dehydrogenase, Fad, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hikima, Y. Kawano, Y. Nodake, N. Kamiya
Crystal Structure Of Acyl Coa Dehydrogenase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE
    Chains: A, B
    EC Number: 1.3.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:146 , LEU A:148 , THR A:149 , GLY A:154 , SER A:155 , TRP A:181 , SER A:183 , ILE A:225 , ILE A:393 , PHE A:397 , ILE A:403 , LEU A:406 , GLN A:476 , HOH A:702 , HOH A:893 , ARG B:289 , PHE B:292 , ILE B:296 , PHE B:299 , ILE B:302 , ILE B:372 , HIS B:373 , GLY B:374 , GLY B:375BINDING SITE FOR RESIDUE FAD A 700
2AC2SOFTWAREARG A:289 , GLN A:291 , PHE A:292 , ILE A:296 , PHE A:299 , ILE A:302 , ILE A:372 , HIS A:373 , GLY A:374 , GLY A:375 , HOH A:857 , ILE B:116 , TYR B:146 , LEU B:148 , THR B:149 , GLY B:154 , SER B:155 , TRP B:181 , SER B:183 , ILE B:225 , ILE B:393 , PHE B:397 , GLU B:402 , ILE B:403 , LEU B:406 , GLN B:476 , HOH B:702 , HOH B:729 , HOH B:817BINDING SITE FOR RESIDUE FAD B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1Q)

(-) 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:546
 aligned with Q5SJW0_THET8 | Q5SJW0 from UniProtKB/TrEMBL  Length:577

    Alignment length:573
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574   
         Q5SJW0_THET8     5 KKLWQKGGGWLLEVPERVYTPEDFDESVKEIARTTRTFVEREVLPLLERMEHGELELNVPLMRKAGELGLLAIDVPEEYGGLDLPKVISTVVAEELSGSGGFSVTYGAHTSIGTLPLVYFGTEEQKRKYLPKLASGEWIAAYCLTEPGSGSDALAAKTRATLSEDGKHYILNGVKQWISNAGFAHLFTVFAKVDGEHFTAFLVERDTPGLSFGPEEKKMGIKASSTRQVILEDVKVPVENVLGEIGKGHKIAFNVLNVGRYKLGAGAVGGAKRALELSAQYATQRVQFGRPIGRFGLIQQKLGEMASRIYAAESAVYRTVGLIDEALLGKKGPEAVMAGIEEYAVEASIIKVLGSEVLDYVVDEGVQIHGGYGYSQEYPIERAYRDARINRIFEGTNEINRLLIPGMLLRRALKGQLPLMQAAQRLQKELLEPSFEEPEDLELHQVQNLKKLALMVAGLAVQKYGQGVEEEQEVLGAVADILIDAYAAESALLRARRLGGLAPVLARIYLAQALDRAQAGALSVLPRLVEGDEARVVYSAARRLTKREPVDLVALRRQAAEAVLEAGGYPIPR 577
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhh..eeee.....eeeeeeeeeeee......eeeeeeee...eeeeeeee.....eee.............eeeeeeeeeeee...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..---------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1q A   5 KKLWQKGGGWLLEVPERVYTPEDFDESVKEIARTTRTFVEREVLPLLERMEHGELELNVPLMRKAGELGLLAIDVPEEYGGLDLPKVISTVVAEELSGSGGFSVTYGAHTSIGTLPLVYFGTEEQKRKYLPKLASGEWIAAYCLTEPGSGSDALAAKTRATLSEDGKHYILNGVKQWISNAGFAHLFTVFAKVDGEHFTAFLVERDTPGLSFGPEEKKMGIKASSTRQVILEDVKVPVENVLGEIGKGHKIAFNVLNVGRYKLGAGAVGGAKRALELSAQYATQRVQFGRPIGRFGLIQQKLGEMASRIYAAESAVYRTVGLIDEALLGKKGPEAVMAGIEEYAVEASIIKVLGSEVLDYVVDEGVQIHGGYGYSQEYPIERAYRDARINRIFEGTNEINRLLIPGMLLRR---------------------------EDLELHQVQNLKKLALMVAGLAVQKYGQGVEEEQEVLGAVADILIDAYAAESALLRARRLGGLAPVLARIYLAQALDRAQAGALSVLPRLVEGDEARVVYSAARRLTKREPGDLVALRRQAAEAVLEAGGYPIPR 577
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414|        -         -       444       454       464       474       484       494       504       514       524       534       544       554       564       574   
                                                                                                                                                                                                                                                                                                                                                                                                                                                    415                         443                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:549
 aligned with Q5SJW0_THET8 | Q5SJW0 from UniProtKB/TrEMBL  Length:577

    Alignment length:573
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574   
         Q5SJW0_THET8     5 KKLWQKGGGWLLEVPERVYTPEDFDESVKEIARTTRTFVEREVLPLLERMEHGELELNVPLMRKAGELGLLAIDVPEEYGGLDLPKVISTVVAEELSGSGGFSVTYGAHTSIGTLPLVYFGTEEQKRKYLPKLASGEWIAAYCLTEPGSGSDALAAKTRATLSEDGKHYILNGVKQWISNAGFAHLFTVFAKVDGEHFTAFLVERDTPGLSFGPEEKKMGIKASSTRQVILEDVKVPVENVLGEIGKGHKIAFNVLNVGRYKLGAGAVGGAKRALELSAQYATQRVQFGRPIGRFGLIQQKLGEMASRIYAAESAVYRTVGLIDEALLGKKGPEAVMAGIEEYAVEASIIKVLGSEVLDYVVDEGVQIHGGYGYSQEYPIERAYRDARINRIFEGTNEINRLLIPGMLLRRALKGQLPLMQAAQRLQKELLEPSFEEPEDLELHQVQNLKKLALMVAGLAVQKYGQGVEEEQEVLGAVADILIDAYAAESALLRARRLGGLAPVLARIYLAQALDRAQAGALSVLPRLVEGDEARVVYSAARRLTKREPVDLVALRRQAAEAVLEAGGYPIPR 577
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------Acyl-CoA_dh_N-2z1qB05 B:29-141                                                                                   ---Acyl-CoA_dh_M-2z1qB03 B:145-199                        --------------------------------------------------Acyl-CoA_dh_1-2z1qB01 B:250-413                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------Acyl-CoA_dh_N-2z1qB06 B:29-141                                                                                   ---Acyl-CoA_dh_M-2z1qB04 B:145-199                        --------------------------------------------------Acyl-CoA_dh_1-2z1qB02 B:250-413                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhh..eeee.....eeeeeeeeeeee......eeeeeeee...eeeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..------------------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1q B   5 KKLWQKGGGWLLEVPERVYTPEDFDESVKEIARTTRTFVEREVLPLLERMEHGELELNVPLMRKAGELGLLAIDVPEEYGGLDLPKVISTVVAEELSGSGGFSVTYGAHTSIGTLPLVYFGTEEQKRKYLPKLASGEWIAAYCLTEPGSGSDALAAKTRATLSEDGKHYILNGVKQWISNAGFAHLFTVFAKVDGEHFTAFLVERDTPGLSFGPEEKKMGIKASSTRQVILEDVKVPVENVLGEIGKGHKIAFNVLNVGRYKLGAGAVGGAKRALELSAQYATQRVQFGRPIGRFGLIQQKLGEMASRIYAAESAVYRTVGLIDEALLGKKGPEAVMAGIEEYAVEASIIKVLGSEVLDYVVDEGVQIHGGYGYSQEYPIERAYRDARINRIFEGTNEINRLLIPGMLLRRA------------------------EPEDLELHQVQNLKKLALMVAGLAVQKYGQGVEEEQEVLGAVADILIDAYAAESALLRARRLGGLAPVLARIYLAQALDRAQAGALSVLPRLVEGDEARVVYSAARRLTKREPGDLVALRRQAAEAVLEAGGYPIPR 577
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414 |       -         -      |444       454       464       474       484       494       504       514       524       534       544       554       564       574   
                                                                                                                                                                                                                                                                                                                                                                                                                                                     416                      441
   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 2Z1Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z1Q)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: Acyl-CoA_dh (32)
(-)
Clan: no clan defined [family: Acyl-CoA_dh_M] (24)
(-)
Clan: no clan defined [family: Acyl-CoA_dh_N] (23)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SJW0_THET8 | Q5SJW0)
molecular function
    GO:0003995    acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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