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(-) Description

Title :  CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM SULFOLOBUS TOKODAII STRAIN 7
 
Authors :  T. Kouyama, H. Kondo
Date :  22 Dec 06  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadp-Dependent Isocitrate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kouyama, H. Kondo
Isocitrate Dehydrogenase From Sulfolobus Tokodaii Strain 7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 409AA LONG HYPOTHETICAL NADP-DEPENDENT ISOCITRATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETAGAMI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS TOKODAII STR. 7
    Organism Taxid: 273063
    Strain: STRAIN 7
    Synonym: ISOCITRATE DEHYDROGENASE

 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
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:35 , LYS A:96 , PRO A:98 , LEU A:99 , THR A:101 , ASN A:111 , GLU A:327 , HIS A:330 , GLY A:331 , THR A:332 , LYS A:335 , TYR A:336 , ASN A:343 , ARG A:386BINDING SITE FOR RESIDUE NAP A 450
2AC2SOFTWAREILE B:35 , LEU B:99 , GLU B:100 , THR B:101 , ASN B:111 , GLU B:327 , HIS B:330 , GLY B:331 , THR B:332 , ALA B:333 , LYS B:335 , TYR B:336 , ASN B:343 , ASP B:383 , ARG B:386 , HOH B:457 , HOH B:616BINDING SITE FOR RESIDUE NAP B 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E5M)

(-) Exons   (0, 0)

(no "Exon" information available for 2E5M)

(-) 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:403
 aligned with Q96YK6_SULTO | Q96YK6 from UniProtKB/TrEMBL  Length:409

    Alignment length:409
                                    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       400         
         Q96YK6_SULTO     1 MLYKEPEDGEKIKFDKGKWIVPNKPVILYIEGDGIGPEITNAAIKVINKAVERAYGSSREIKWLEVYAGEKAEKLVNDRFPKETQEMLLKYRVVLKGPLETPIGKGWKSVNVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEYPFNSEEAKKIRDFLRKELKVEIEDDTGIGIKVMSKYKTQRITRLAIQYAIEHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEYRDFIVTEEEINQGKPDQGKIILNDRIADNMFQQIIIRPEEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDEGGMFEAIHGTAPKYAGKNVANPTGIIKAGELMLRWMGWNEAADLIEKAINMAIRDKKVTQDIARFMGVKALGTKEYADELIKIMDTI 409
               SCOP domains d2e5ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2e5mA00 A:1-409 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhh...hhhhhhhhhhhheeee......------hhhhhhhhhhh..eeeeeee...............eeeeeee..hhhhhh.ee...hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh...eeehhhhh........eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh..hhhh.eeeeee..eeeeee....hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e5m A   1 MLYKEPEDGEKIKFDKGKWIVPNKPVILYIEGDGIGPEITNAAIKVINKAVERAYGSSREIKWLEVYAGEKAEKLVNDRFPKETQEMLLKYRVVLKGPLETP------SVNVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEYPFNSEEAKKIRDFLRKELKVEIEDDTGIGIKVMSKYKTQRITRLAIQYAIEHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEYRDFIVTEEEINQGKPDQGKIILNDRIADNMFQQIIIRPEEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDEGGMFEAIHGTAPKYAGKNVANPTGIIKAGELMLRWMGWNEAADLIEKAINMAIRDKKVTQDIARFMGVKALGTKEYADELIKIMDTI 409
                                    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       400         
                                                                                                                               102    109                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:403
 aligned with Q96YK6_SULTO | Q96YK6 from UniProtKB/TrEMBL  Length:409

    Alignment length:409
                                    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       400         
         Q96YK6_SULTO     1 MLYKEPEDGEKIKFDKGKWIVPNKPVILYIEGDGIGPEITNAAIKVINKAVERAYGSSREIKWLEVYAGEKAEKLVNDRFPKETQEMLLKYRVVLKGPLETPIGKGWKSVNVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEYPFNSEEAKKIRDFLRKELKVEIEDDTGIGIKVMSKYKTQRITRLAIQYAIEHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEYRDFIVTEEEINQGKPDQGKIILNDRIADNMFQQIIIRPEEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDEGGMFEAIHGTAPKYAGKNVANPTGIIKAGELMLRWMGWNEAADLIEKAINMAIRDKKVTQDIARFMGVKALGTKEYADELIKIMDTI 409
               SCOP domains d2e5mb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2e5mB00 B:1-409 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee....ee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhh...hhhhhhhhhhhheeee......------hhhhhhhhhh...eeeeeee...............eeeeeee..hhhhhh.ee...hhhhhhhhhhhhhhh.......eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh...eeehhhhh........eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh..hhhh.eeeeee..eeeeee....hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e5m B   1 MLYKEPEDGEKIKFDKGKWIVPNKPVILYIEGDGIGPEITNAAIKVINKAVERAYGSSREIKWLEVYAGEKAEKLVNDRFPKETQEMLLKYRVVLKGPLETP------SVNVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEYPFNSEEAKKIRDFLRKELKVEIEDDTGIGIKVMSKYKTQRITRLAIQYAIEHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEYRDFIVTEEEINQGKPDQGKIILNDRIADNMFQQIIIRPEEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDEGGMFEAIHGTAPKYAGKNVANPTGIIKAGELMLRWMGWNEAADLIEKAINMAIRDKKVTQDIARFMGVKALGTKEYADELIKIMDTI 409
                                    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       400         
                                                                                                                               102    109
   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  (0, 0)

(no "Pfam Domain" information available for 2E5M)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q96YK6_SULTO | Q96YK6)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004450    isocitrate dehydrogenase (NADP+) activity    Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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: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
        Q96YK6_SULTO | Q96YK6: 2dht 2e0c

(-) Related Entries Specified in the PDB File

2e0c THE SAME PROTEIN WITHOUT NADP+