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(-) Description

Title :  ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE THERMOTOGA MARITIMA
 
Authors :  M. Karlstrom, I. H. Steen, N. -K. Birkeland, R. Ladenstein
Date :  13 May 05  (Deposition) - 16 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wild Type Enzyme, Cis-Proline, Thermostable, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Karlstrom, I. H. Steen, D. Madern, A. E. Fedoy, N. K. Birkeland, R. Ladenstein
The Crystal Structure Of A Hyperthermostable Subfamily Ii Isocitrate Dehydrogenase From Thermotoga Maritima.
Febs J. V. 273 2851 2006
PubMed-ID: 16759231  |  Reference-DOI: 10.1111/J.1742-4658.2006.05298.X

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1148
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:270 , ASP A:274 , HOH A:1160 , HOH A:1347 , ASP B:247BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWAREASP A:247 , ASP B:270 , ASP B:274 , HOH B:1055 , HOH B:1056BINDING SITE FOR RESIDUE NA B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:375 -Pro A:376
2Glu B:375 -Pro B:376

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZOR)

(-) 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:399
 aligned with Q9X0N2_THEMA | Q9X0N2 from UniProtKB/TrEMBL  Length:399

    Alignment length:399
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390         
         Q9X0N2_THEMA     1 MEKVKVKNPIVELDGDEMARVMWKMIKEKLILPYLDIQLVYFDLGIKKRDETDDQITIEAAKAIKKYGVGVKCATITPDAERVKEYNLKKAWKSPNATIRAYLDGTVFRKPIMVKNVPPLVKRWKKPIIIGRHAYGDIYNAVEAKVEGPAEVELVVRNKENKTLLVHKFEGNGVVMAMHNLEKSIRSFAQSCINYAISEKVDIWFATKDTISKVYHAYFKDIFQEEVDKRKEELEKAGVNYRYMLIDDAAAQILRSEGGMLWACMNYEGDIMSDMIASGFGSLGLMTSVLVSPDGVYEFEAAHGTVRRHYYRYLKGEKTSTNPTASIFAWTGAIRKRGELDGTPEVCEFADKLEKAVINTIESGVITKDLQPFTEPPIDKYVTLEEFIDEVKKNLEKLL 399
               SCOP domains d1zora_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1zorA00 A:1-399 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee...hhhhhheeeee...eeeeeeee....eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zor A   1 MEKVKVKNPIVELDGDEMARVMWKMIKEKLILPYLDIQLVYFDLGIKKRDETDDQITIEAAKAIKKYGVGVKCATITPDAERVKEYNLKKAWKSPNATIRAYLDGTVFRKPIMVKNVPPLVKRWKKPIIIGRHAYGDIYNAVEAKVEGPAEVELVVRNKENKTLLVHKFEGNGVVMAMHNLEKSIRSFAQSCINYAISEKVDIWFATKDTISKVYHAYFKDIFQEEVDKRKEELEKAGVNYRYMLIDDAAAQILRSEGGMLWACMNYEGDIMSDMIASGFGSLGLMTSVLVSPDGVYEFEAAHGTVRRHYYRYLKGEKTSTNPTASIFAWTGAIRKRGELDGTPEVCEFADKLEKAVINTIESGVITKDLQPFTEPPIDKYVTLEEFIDEVKKNLEKLL 399
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390         


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with Q9X0N2_THEMA | Q9X0N2 from UniProtKB/TrEMBL  Length:399

    Alignment length:396
                                    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      
         Q9X0N2_THEMA     4 VKVKNPIVELDGDEMARVMWKMIKEKLILPYLDIQLVYFDLGIKKRDETDDQITIEAAKAIKKYGVGVKCATITPDAERVKEYNLKKAWKSPNATIRAYLDGTVFRKPIMVKNVPPLVKRWKKPIIIGRHAYGDIYNAVEAKVEGPAEVELVVRNKENKTLLVHKFEGNGVVMAMHNLEKSIRSFAQSCINYAISEKVDIWFATKDTISKVYHAYFKDIFQEEVDKRKEELEKAGVNYRYMLIDDAAAQILRSEGGMLWACMNYEGDIMSDMIASGFGSLGLMTSVLVSPDGVYEFEAAHGTVRRHYYRYLKGEKTSTNPTASIFAWTGAIRKRGELDGTPEVCEFADKLEKAVINTIESGVITKDLQPFTEPPIDKYVTLEEFIDEVKKNLEKLL 399
               SCOP domains d1zorb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1zorB00 B:4-399 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -Iso_dh-1zorB01 B:5-391                                                                                                                                                                                                                                                                                                                                                                             -------- Pfam domains (1)
           Pfam domains (2) -Iso_dh-1zorB02 B:5-391                                                                                                                                                                                                                                                                                                                                                                             -------- Pfam domains (2)
         Sec.struct. author ......eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee...hhhhhheeeee...eeeeeeeee...eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zor B   4 VKVKNPIVELDGDEMARVMWKMIKEKLILPYLDIQLVYFDLGIKKRDETDDQITIEAAKAIKKYGVGVKCATITPDAERVKEYNLKKAWKSPNATIRAYLDGTVFRKPIMVKNVPPLVKRWKKPIIIGRHAYGDIYNAVEAKVEGPAEVELVVRNKENKTLLVHKFEGNGVVMAMHNLEKSIRSFAQSCINYAISEKVDIWFATKDTISKVYHAYFKDIFQEEVDKRKEELEKAGVNYRYMLIDDAAAQILRSEGGMLWACMNYEGDIMSDMIASGFGSLGLMTSVLVSPDGVYEFEAAHGTVRRHYYRYLKGEKTSTNPTASIFAWTGAIRKRGELDGTPEVCEFADKLEKAVINTIESGVITKDLQPFTEPPIDKYVTLEEFIDEVKKNLEKLL 399
                                    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
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X0N2_THEMA | Q9X0N2)
molecular function
    GO:0004450    isocitrate dehydrogenase (NADP+) activity    Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0006102    isocitrate metabolic process    The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
    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.
    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.

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