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(-) Description

Title :  CRYSTAL STRUCTURE OF PROJECT TT0160 FROM THERMUS THERMOPHILUS HB8
 
Authors :  K. Shimizu, Riken Structural Genomics/Proteomics Initiative (R
Date :  31 Jul 06  (Deposition) - 31 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  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
Crystal Structure Of Tt0160 From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: ACYL-COA DEHYDROGENASE, SHORT-CHAIN SPECIFIC

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (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, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:121 , LEU A:123 , THR A:124 , GLY A:129 , SER A:130 , TRP A:154 , ILE A:155 , THR A:156 , ARG A:261 , GLN A:263 , PHE A:264 , LEU A:268 , HIS A:271 , ILE A:274 , GLN A:329 , VAL A:330 , GLY A:333 , VAL A:351 , THR A:358 , GLU A:360 , HOH A:1005 , HOH A:1059 , GLN B:272BINDING SITE FOR RESIDUE FAD A 1001
2AC2SOFTWAREGLN A:272 , PHE B:121 , LEU B:123 , THR B:124 , GLY B:129 , SER B:130 , TRP B:154 , THR B:156 , ARG B:261 , GLN B:263 , PHE B:264 , LEU B:268 , HIS B:271 , GLN B:329 , VAL B:330 , GLY B:332 , GLY B:333 , TYR B:334 , THR B:358 , GLU B:360 , HOH B:1005 , HOH B:1029 , HOH B:1042 , HOH B:1088BINDING SITE FOR RESIDUE FAD B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DVL)

(-) 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:370
 aligned with Q5SH14_THET8 | Q5SH14 from UniProtKB/TrEMBL  Length:372

    Alignment length:370
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
         Q5SH14_THET8     3 LTQEQRLVLDAVRRVAREVLYPLAPEYDRKAEYPWPQLKALAELGLLGMTTPEEWGGVGLDSVTWALALEELAAADPSVAVIVSVTSGLPQYMLLRFGSEAQKRRYLVPLARGEWIGAFCLTEPQAGSDAKSLRAEARRVKGGFVLNGVKSWITSAGHAHLYVVMARTEKGISAFLVEKGTPGLSFGRPEEKMGLHAAHTAEVRLEEVFVPEENLLGEEGRGLAYALAGLDSGRVGVAAQAVGIARGAFEIAKAYAEEREQFGKKLKEHQAIAFKIADMHVKIAAARALVLEAARKKDRGERFTLEASAAKLFASAAAVEVTREAVQVLGGYGYHRDYRVERYYRDAKVTEIYEGTSEIQRLVIARELYR 372
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dvlA01 A:3-118 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                      2dvlA02 A:119-220 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                      --2dvlA03 A:223-371 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                     - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..eeeee..eeeeeeeeeeee......eeeeeeee..eeeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvl A   3 LTQEQRLVLDAVRRVAREVLYPLAPEYDRKAEYPWPQLKALAELGLLGMTTPEEWGGVGLDSVTWALALEELAAADPSVAVIVSVTSGLPQYMLLRFGSEAQKRRYLVPLARGEWIGAFCLTEPQAGSDAKSLRAEARRVKGGFVLNGVKSWITSAGHAHLYVVMARTEKGISAFLVEKGTPGLSFGRPEEKMGLHAAHTAEVRLEEVFVPEENLLGEEGRGLAYALAGLDSGRVGVAAQAVGIARGAFEIAKAYAEEREQFGKKLKEHQAIAFKIADMHVKIAAARALVLEAARKKDRGERFTLEASAAKLFASAAAVEVTREAVQVLGGYGYHRDYRVERYYRDAKVTEIYEGTSEIQRLVIARELYR 372
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372


Chain B from PDB  Type:PROTEIN  Length:370
 aligned with Q5SH14_THET8 | Q5SH14 from UniProtKB/TrEMBL  Length:372

    Alignment length:370
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
         Q5SH14_THET8     3 LTQEQRLVLDAVRRVAREVLYPLAPEYDRKAEYPWPQLKALAELGLLGMTTPEEWGGVGLDSVTWALALEELAAADPSVAVIVSVTSGLPQYMLLRFGSEAQKRRYLVPLARGEWIGAFCLTEPQAGSDAKSLRAEARRVKGGFVLNGVKSWITSAGHAHLYVVMARTEKGISAFLVEKGTPGLSFGRPEEKMGLHAAHTAEVRLEEVFVPEENLLGEEGRGLAYALAGLDSGRVGVAAQAVGIARGAFEIAKAYAEEREQFGKKLKEHQAIAFKIADMHVKIAAARALVLEAARKKDRGERFTLEASAAKLFASAAAVEVTREAVQVLGGYGYHRDYRVERYYRDAKVTEIYEGTSEIQRLVIARELYR 372
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dvlB01 B:3-118 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                      2dvlB02 B:119-220 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                      --2dvlB03 B:223-371 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                     - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..eeeee..eeeeeeeeeeee......eeeeeeee..eeeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvl B   3 LTQEQRLVLDAVRRVAREVLYPLAPEYDRKAEYPWPQLKALAELGLLGMTTPEEWGGVGLDSVTWALALEELAAADPSVAVIVSVTSGLPQYMLLRFGSEAQKRRYLVPLARGEWIGAFCLTEPQAGSDAKSLRAEARRVKGGFVLNGVKSWITSAGHAHLYVVMARTEKGISAFLVEKGTPGLSFGRPEEKMGLHAAHTAEVRLEEVFVPEENLLGEEGRGLAYALAGLDSGRVGVAAQAVGIARGAFEIAKAYAEEREQFGKKLKEHQAIAFKIADMHVKIAAARALVLEAARKKDRGERFTLEASAAKLFASAAAVEVTREAVQVLGGYGYHRDYRVERYYRDAKVTEIYEGTSEIQRLVIARELYR 372
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
   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 2DVL)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SH14_THET8 | Q5SH14)
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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