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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ACYL-COA DEHYDROGENASE FAMILY PROTEIN FROM PORPHYROMONAS GINGIVALIS
 
Authors :  R. Zhang, L. Bigelow, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  17 Jan 07  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  The Acyl-Coa Dehydrogenase, Porphyromonas Gingivalis, Psi-2, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, L. Bigelow, J. Abdullah, A. Joachimiak
The Crystal Structure Of The Acyl-Coa Dehydrogenase Family Protein From Porphyromonas Gingivalis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE FAMILY PROTEIN
    Atcc: BAA-308
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 443-573
    Gene: PG_0775
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OKU)

(-) 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:122
 aligned with Q7MW70_PORGI | Q7MW70 from UniProtKB/TrEMBL  Length:573

    Alignment length:122
                                   452       462       472       482       492       502       512       522       532       542       552       562  
         Q7MW70_PORGI   443 QVVAAIRHITTGTYIARIREEYQQTEVKPELQPMKEALARMTDRAEALIAFVTEQKDQELLDFQARRLVEMTAHAVFGHLLMLAANDDDSFRQSAEVYLRYGQAEQEKIDSYVRAFRPEELT 564
               SCOP domains d2okua1 A:443-564 Uncharacterized protein PG0775                                                                           SCOP domains
               CATH domains 2okuA00 A:443-564 PG0775 C-terminal domain-like                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oku A 443 QVVAAIRHITTGTYIARIREEYQQTEVKPELQPmKEALARmTDRAEALIAFVTEQKDQELLDFQARRLVEmTAHAVFGHLLmLAANDDDSFRQSAEVYLRYGQAEQEKIDSYVRAFRPEELT 564
                                   452       462       472   |   482|      492       502       512|      522 |     532       542       552       562  
                                                           476-MSE  |                           513-MSE    524-MSE                                    
                                                                  483-MSE                                                                             


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q7MW70_PORGI | Q7MW70 from UniProtKB/TrEMBL  Length:573

    Alignment length:116
                                   454       464       474       484       494       504       514       524       534       544       554      
         Q7MW70_PORGI   445 VAAIRHITTGTYIARIREEYQQTEVKPELQPMKEALARMTDRAEALIAFVTEQKDQELLDFQARRLVEMTAHAVFGHLLMLAANDDDSFRQSAEVYLRYGQAEQEKIDSYVRAFRP 560
               SCOP domains d2okub_ B: Uncharacterized protein PG0775                                                                            SCOP domains
               CATH domains 2okuB00 B:445-560 PG0775 C-terminal domain-like                                                                      CATH domains
           Pfam domains (1) Acyl-CoA------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Acyl-CoA------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -------AcylCoA_dehyd_C-2okuB03 B:452-560                                                                             Pfam domains (3)
           Pfam domains (4) -------AcylCoA_dehyd_C-2okuB04 B:452-560                                                                             Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2oku B 445 VAAIRHITTGTYIARIREEYQQTEVKPELQPmKEALARmTDRAEALIAFVTEQKDQELLDFQARRLVEmTAHAVFGHLLmLAANDDDSFRQSAEVYLRYGQAEQEKIDSYVRAFRP 560
                                   454       464       474 |     484       494       504       514       524       534       544       554      
                                                         476-MSE  |                           513-MSE    524-MSE                                
                                                                483-MSE
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Acyl-CoA_dh (32)
(-)
Clan: no clan defined [family: AcylCoA_dehyd_C] (1)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7MW70_PORGI | Q7MW70)
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: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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