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(-) Description

Title :  2.2 A CRYSTAL STRUCTURE OF GLUTARYL-COA DEHYDROGENASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  19 May 08  (Deposition) - 03 Jun 08  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Burkholderia, Pseudomallei, Glutaryl-Coa, Dehydrogenase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Fad, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Begley, D. R. Davies, R. C. Hartley, S. N. Hewitt, A. L. Rychel, P. J. Myler, W. C. Van Voorhis, B. L. Staker, L. J. Stewart
Probing Conformational States Of Glutaryl-Coa Dehydrogenase By Fragment Screening.
Acta Crystallogr. , Sect. F V. 67 1060 2011
PubMed-ID: 21904051  |  Reference-DOI: 10.1107/S1744309111014436

(-) Compounds

Molecule 1 - GLUTARYL-COA DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.3.99.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BURPS1710B_3237
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
154D1Ligand/IonMETHYL THIOPHENE-2-CARBOXYLATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:98 , ILE C:257 , TYR C:373 , GLU C:374BINDING SITE FOR RESIDUE 54D C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D6B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly B:159 -Gly B:160
2Asp C:188 -Gly C:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D6B)

(-) Exons   (0, 0)

(no "Exon" information available for 3D6B)

(-) 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 Q3JP94_BURP1 | Q3JP94 from UniProtKB/TrEMBL  Length:395

    Alignment length:390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
         Q3JP94_BURP1     4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
               SCOP domains d3d6ba1 A:4-242 automated matches                                                                                                                                                                                                              d3d6ba2 A:243-393 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....--------...eeeee..eeeeeeeeeeee.hhhh.eeeeeeee...---.eeeeeee.....ee..ee..........eeeeeeeeeeee.hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh-----hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d6b A   4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEP--------MVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED---EIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTY-----IHALILGRAQTGIQA 393
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       | -      |153       163       173       183    |  193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373     | 383       393
                                                                                                                                                                   141      150                                   188 192                                                                                                                                                                                  373   379              


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with Q3JP94_BURP1 | Q3JP94 from UniProtKB/TrEMBL  Length:395

    Alignment length:390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
         Q3JP94_BURP1     4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
               SCOP domains d3d6bb1 B:4-242 automated matches                                                                                                                                                                                                              d3d6bb2 B:243-393 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....--------...........eeeeeeeeeee.hhhh.eeeeeeee..---.eeeeeeee.....ee..............eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.--------hhhhhhhhhhhhhhh....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d6b B   4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEP--------MVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDE---DEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDR------LAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLG--------GVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       | -      |153       163       173       183   |   193       203       213       223       233       243       253       263       273     |   -  |    293       303       313       323       333       343      |  -     | 363       373       383       393
                                                                                                                                                                   141      150                                  187 191                                                                                     279    286                                                             350      359                                  


Chain C from PDB  Type:PROTEIN  Length:377
 aligned with Q3JP94_BURP1 | Q3JP94 from UniProtKB/TrEMBL  Length:395

    Alignment length:390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
         Q3JP94_BURP1     4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
               SCOP domains d3d6bc1 C:4-242 automated matches                                                                                                                                                                                                              d3d6bc2 C:243-393 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......---.....eeeee..eeeeeeeeeeee.hhhh.eeeeeeeee....eeeeeeeee.....ee..............eeeeeeeeeeee.hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.-------hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d6b C   4 ATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHG---GSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQ---PLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLG-------FGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143|   |  153       163       173       183       193       203       213       223       233       243       253       263       273       | - |     293       303       313       323       333       343      |  -    |  363       373       383       393
                                                                                                                                                                      144 148                                                                                                                                  281 285                                                              350     358                                   


Chain D from PDB  Type:PROTEIN  Length:372
 aligned with Q3JP94_BURP1 | Q3JP94 from UniProtKB/TrEMBL  Length:395

    Alignment length:391
                                    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       382       392 
         Q3JP94_BURP1     3 AATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQA 393
               SCOP domains d3d6bd1 D:3-242 automated matches                                                                                                                                                                                                               d3d6bd2 D:243-393 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....-------....eeeee..eeeeeeeeeeee.hhhh.eeeeeeee.----.eeeeeeee.....ee..ee..........eeeeeeeeeeee.hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...------hhhhhhhhhhhhhhh.--.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6b D   3 AATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEP-------SMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD----DEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGN------GVARHLVNLEVVNTYE--HDIHALILGRAQTGIQA 393
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        |-      |152       162       172       182   |   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      |362       372 |  |  382       392 
                                                                                                                                                                    141     149                                  186  191                                                                                                                                                              352    359            374  |                
                                                                                                                                                                                                                                                                                                                                                                                                                377
   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, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D6B)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q3JP94_BURP1 | Q3JP94)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q3JP94_BURP1 | Q3JP94: 3eom 3eon 3gnc 3gqt 3ii9

(-) Related Entries Specified in the PDB File

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