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(-) Description

Title :  STRUCTURAL STUDY ON PROJECT ID TT0172 FROM THERMUS THERMOPHILUS HB8
 
Authors :  K. Shimizu, N. Kunishima, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  05 Sep 05  (Deposition) - 05 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dehydrogenase, 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 :  K. Shimizu, N. Kunishima
Structural Study On Project Id Tt0172 From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 11A
    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 Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:125 , LEU A:127 , THR A:128 , GLY A:133 , SER A:134 , PHE A:158 , ILE A:159 , THR A:160 , LYS A:207 , ARG A:274 , PHE A:277 , ILE A:281 , PHE A:284 , GLN A:342 , ILE A:343 , GLY A:346 , TYR A:347 , LEU A:364 , THR A:371 , GLU A:373 , HOH A:1038 , HOH A:1083 , HOH A:1157 , HOH A:1281 , HOH A:1404 , GLU B:285BINDING SITE FOR RESIDUE FAD A 1001
2AC2SOFTWAREGLU A:285 , TRP B:125 , LEU B:127 , THR B:128 , GLY B:133 , SER B:134 , PHE B:158 , ILE B:159 , THR B:160 , LYS B:207 , ARG B:274 , PHE B:277 , ILE B:281 , PHE B:284 , GLN B:342 , ILE B:343 , GLY B:346 , TYR B:347 , LEU B:364 , THR B:371 , GLU B:373 , HOH B:2012 , HOH B:2028 , HOH B:2054BINDING SITE FOR RESIDUE FAD B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D29)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D29)

(-) Exons   (0, 0)

(no "Exon" information available for 2D29)

(-) 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:386
 aligned with Q5SGZ2_THET8 | Q5SGZ2 from UniProtKB/TrEMBL  Length:387

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
         Q5SGZ2_THET8     2 GLWFEEGAEERQVLGPFREFLKAEVAPGAAERDRTGAFPWDLVRKLAEFGVFGALVPEAYGGAGLSTRLFARMVEAIAYYDGALALTVASHNSLATGHILLAGSEAQKEAFLPKLASGEALGAWGLTEPGSGSDAAALKTKAEKVEGGWRLNGTKQFITQGSVAGVYVVMARTDPPPSPERKHQGISAFAFFRPERGLKVGRKEEKLGLTASDTAQLILEDLFVPEEALLGERGKGFYDVLRVLDGGRIGIAAMAVGLGQAALDYALAYAKGREAFGRPIAEFEGVSFKLAEAATELEAARLLYLKAAELKDAGRPFTLEAAQAKLFASEAAVKACDEAIQILGGYGYVKDYPVERYWRDARLTRIGEGTSEILKLVIARRLLEAV 387
               SCOP domains d2d29a2 A:2-234 Acyl-CoA dehydrogenase                                                                                                                                                                                                   d2d29a1 A:235-387 Acyl-CoA dehydrogenase                                                                                                                  SCOP domains
               CATH domains ---2d29A01 A:5-122 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                        2d29A02 A:123-233 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                               --2d29A03 A:236-384 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..eeeee..eeeeeeeeeeee......eeeeeee.....hhhhh...eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d29 A   2 GLWFEEGAEERQVLGPFREFLKAEVAPGAAERDRTGAFPWDLVRKLAEFGVFGALVPEAYGGAGLSTRLFARMVEAIAYYDGALALTVASHNSLATGHILLAGSEAQKEAFLPKLASGEALGAWGLTEPGSGSDAAALKTKAEKVEGGWRLNGTKQFITQGSVAGVYVVMARTDPPPSPERKHQGISAFAFFRPERGLKVGRKEEKLGLTASDTAQLILEDLFVPEEALLGERGKGFYDVLRVLDGGRIGIAAMAVGLGQAALDYALAYAKGREAFGRPIAEFEGVSFKLAEAATELEAARLLYLKAAELKDAGRPFTLEAAQAKLFASEAAVKACDEAIQILGGYGYVKDYPVERYWRDARLTRIGEGTSEILKLVIARRLLEAV 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q5SGZ2_THET8 | Q5SGZ2 from UniProtKB/TrEMBL  Length:387

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
         Q5SGZ2_THET8     2 GLWFEEGAEERQVLGPFREFLKAEVAPGAAERDRTGAFPWDLVRKLAEFGVFGALVPEAYGGAGLSTRLFARMVEAIAYYDGALALTVASHNSLATGHILLAGSEAQKEAFLPKLASGEALGAWGLTEPGSGSDAAALKTKAEKVEGGWRLNGTKQFITQGSVAGVYVVMARTDPPPSPERKHQGISAFAFFRPERGLKVGRKEEKLGLTASDTAQLILEDLFVPEEALLGERGKGFYDVLRVLDGGRIGIAAMAVGLGQAALDYALAYAKGREAFGRPIAEFEGVSFKLAEAATELEAARLLYLKAAELKDAGRPFTLEAAQAKLFASEAAVKACDEAIQILGGYGYVKDYPVERYWRDARLTRIGEGTSEILKLVIARRLLEAV 387
               SCOP domains d2d29b2 B:2-234 Acyl-CoA dehydrogenase                                                                                                                                                                                                   d2d29b1 B:235-387 Acyl-CoA dehydrogenase                                                                                                                  SCOP domains
               CATH domains ---2d29B01 B:5-122 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                        2d29B02 B:123-233 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                               --2d29B03 B:236-384 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..eeeee..eeeeeeeeeeee......eeeeeee.....hhhhh...eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d29 B   2 GLWFEEGAEERQVLGPFREFLKAEVAPGAAERDRTGAFPWDLVRKLAEFGVFGALVPEAYGGAGLSTRLFARMVEAIAYYDGALALTVASHNSLATGHILLAGSEAQKEAFLPKLASGEALGAWGLTEPGSGSDAAALKTKAEKVEGGWRLNGTKQFITQGSVAGVYVVMARTDPPPSPERKHQGISAFAFFRPERGLKVGRKEEKLGLTASDTAQLILEDLFVPEEALLGERGKGFYDVLRVLDGGRIGIAAMAVGLGQAALDYALAYAKGREAFGRPIAEFEGVSFKLAEAATELEAARLLYLKAAELKDAGRPFTLEAAQAKLFASEAAVKACDEAIQILGGYGYVKDYPVERYWRDARLTRIGEGTSEILKLVIARRLLEAV 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D29)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SGZ2_THET8 | Q5SGZ2)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q5SGZ2_THET8 | Q5SGZ2: 1ws9 2cx9

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