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(-) Description

Title :  CRYSTAL STRUCTURE OF FUMARASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Mar 04  (Deposition) - 13 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Fumarase, Tca Cycle, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of Fumarase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FUMARATE HYDRATASE CLASS II
    Chains: A, B
    EC Number: 4.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: FUMARASE C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VDK)

(-) Sites  (0, 0)

(no "Site" information available for 1VDK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VDK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:301 -Pro A:302
2Gly B:301 -Pro B:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VDK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VDK)

(-) Exons   (0, 0)

(no "Exon" information available for 1VDK)

(-) 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:458
 aligned with P84127_THETH | P84127 from UniProtKB/TrEMBL  Length:466

    Alignment length:460
                                    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       403       413       423       433       443       453       463
         P84127_THETH     4 RIERDTMGEVRVPADKYWGAQTQRSLENFRIGTDRFRMPLEIIRAYGMLKKAAARANLELGELPEEIAKAIIQAAEEVVQGKWDDHFPLVVFQTGSGTQTNMNVNEVIANRASEILGKPLGSKYAHPNDHVNRGQSSNDTFPTAMYVAVALALHQRLYPAVEGLIRTFTAKAQAFDQIVKVGRTHLMDAVPITLGQEIGSWAAQLKTTLAAVKEMEKGLYNLAIGGTAVGTGLNAHPRFGELVAKYLAEETGLPFRVAENRFAALAAHDELVNVMGAIRTLAGALMKIGNDVRWLASGPYAGIGEITIPANEPGSSIMPGKVNPTQVEALTMVVVRVYGNDHTVAFAGSQGNFQLNVYKPVMAYSTLESINLLADAVASFDAHLAQGIEPNLERIEEYLQKNPMLATALNKAIGYDKAAEIVKKALKEKKTLKQAALELGYLTEEEFDRIVVPMRLAKPH 463
               SCOP domains d1vdka_ A: Fumarase                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vdkA01 A:4-138 Fumarase/aspartase (N-terminal domain)                                                                                 1vdkA02 A:139-404 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                     1vdkA03 A:405-463 Fumarase  /aspartase (C-terminal domain)  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.......hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......--.hhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdk A   4 RIERDTMGEVRVPADKYWGAQTQRSLENFRIGTDRFRMPLEIIRAYGMLKKAAARANLELGELPEEIAKAIIQAAEEVVQGKWDDHFPLVVFQTGSGTQTNMNVNEVIANRASEILGKPLGSKYAHPNDHVNRGQSSNDTFPTAMYVAVALALHQRLYPAVEGLIRTFTAKAQAFDQIVKVGRTHLMDAVPITLGQEIGSWAAQLKTTLAAVKEMEKGLYNLAIGGTAVGTGLNAHPRFGELVAKYLAEETGLPFRVAENRFAALAAHDELVNVMGAIRTLAGALMKIGNDVRWLASGPYAGIGEITIPANEPGSSIMPGKVNPTQVEALTMVVVRVYGNDHTVAFAGSQGNFQLNVYKPVMAYSTLESINLLADAVASFDAHLAQGIEPNLERIEEYLQKNPMLATALNKAIGYDKAAEIVKKALK--KTLKQAALELGYLTEEEFDRIVVPMRLAKPH 463
                                    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       403       413       423      |433       443       453       463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    430  |                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       433                              


Chain B from PDB  Type:PROTEIN  Length:457
 aligned with P84127_THETH | P84127 from UniProtKB/TrEMBL  Length:466

    Alignment length:460
                                    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       403       413       423       433       443       453       463
         P84127_THETH     4 RIERDTMGEVRVPADKYWGAQTQRSLENFRIGTDRFRMPLEIIRAYGMLKKAAARANLELGELPEEIAKAIIQAAEEVVQGKWDDHFPLVVFQTGSGTQTNMNVNEVIANRASEILGKPLGSKYAHPNDHVNRGQSSNDTFPTAMYVAVALALHQRLYPAVEGLIRTFTAKAQAFDQIVKVGRTHLMDAVPITLGQEIGSWAAQLKTTLAAVKEMEKGLYNLAIGGTAVGTGLNAHPRFGELVAKYLAEETGLPFRVAENRFAALAAHDELVNVMGAIRTLAGALMKIGNDVRWLASGPYAGIGEITIPANEPGSSIMPGKVNPTQVEALTMVVVRVYGNDHTVAFAGSQGNFQLNVYKPVMAYSTLESINLLADAVASFDAHLAQGIEPNLERIEEYLQKNPMLATALNKAIGYDKAAEIVKKALKEKKTLKQAALELGYLTEEEFDRIVVPMRLAKPH 463
               SCOP domains d1vdkb_ B: Fumarase                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vdkB01 B:4-138 Fumarase/aspartase (N-terminal domain)                                                                                 1vdkB02 B:139-404 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                     1vdkB03 B:405-463 Fumarase/aspartase (C-terminal domain)    CATH domains
           Pfam domains (1) -------Lyase_1-1vdkB03 B:11-342                                                                                                                                                                                                                                                                                                                    -----------------------------------------------------------------FumaraseC_C-1vdkB01 B:408-462                          - Pfam domains (1)
           Pfam domains (2) -------Lyase_1-1vdkB04 B:11-342                                                                                                                                                                                                                                                                                                                    -----------------------------------------------------------------FumaraseC_C-1vdkB02 B:408-462                          - Pfam domains (2)
         Sec.struct. author .eeee..eeee.......hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee......---.......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdk B   4 RIERDTMGEVRVPADKYWGAQTQRSLENFRIGTDRFRMPLEIIRAYGMLKKAAARANLELGELPEEIAKAIIQAAEEVVQGKWDDHFPLVVFQTGSGTQTNMNVNEVIANRASEILGKPLGSKYAHPNDHVNRGQSSNDTFPTAMYVAVALALHQRLYPAVEGLIRTFTAKAQAFDQIVKVGRTHLMDAVPITLGQEIGSWAAQLKTTLAAVKEMEKGLYNLAIGGTAVGTGLNAHPRFGELVAKYLAEETGLPFRVAENRFAALAAHDELVNVMGAIRTLAGALMKIGNDVRWLASGPYAGIGEITIPANEP---IMPGKVNPTQVEALTMVVVRVYGNDHTVAFAGSQGNFQLNVYKPVMAYSTLESINLLADAVASFDAHLAQGIEPNLERIEEYLQKNPMLATALNKAIGYDKAAEIVKKALKEKKTLKQAALELGYLTEEEFDRIVVPMRLAKPH 463
                                    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       403       413       423       433       443       453       463
                                                                                                                                                                                                                                                                                                                                                  316 320
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: FumaraseC_C] (10)
(-)
Clan: no clan defined [family: Lyase_1] (27)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P84127_THETH | P84127)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004333    fumarate hydratase activity    Catalysis of the reaction: (S)-malate = fumarate + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006106    fumarate metabolic process    The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045239    tricarboxylic acid cycle enzyme complex    Any of the heteromeric enzymes that act in the TCA cycle.

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