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(-) Description

Title :  TERNARY COMPLEX OF ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE AEROPYRUM PERNIX
 
Authors :  M. Karlstrom, R. Stokke, I. H. Steen, N. -K. Birkeland, R. Ladenstein
Date :  28 Sep 04  (Deposition) - 04 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Ternary Complex, Isocitrate, Ca2+, Nadp+, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Karlstrom, R. Stokke, I. H. Steen, N. -K. Birkeland, R. Ladenstein
Isocitrate Dehydrogenase From The Hyperthermophile Aeropyru Pernix: X-Ray Structure Analysis Of A Ternary Enzyme-Substrate Complex And Thermal Stability.
J. Mol. Biol. V. 345 559 2005
PubMed-ID: 15581899  |  Reference-DOI: 10.1016/J.JMB.2004.10.025

(-) 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: BAA79665
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ICT2Ligand/IonISOCITRIC ACID
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:287 , ASP B:311 , ICT B:1004 , HOH B:1005 , HOH B:1006BINDING SITE FOR RESIDUE CA A 1005
2AC2SOFTWAREASP A:311 , ASP A:315 , ICT A:1002 , HOH A:1135 , HOH A:1136 , HOH A:1137 , ASP B:287BINDING SITE FOR RESIDUE CA A 1006
3AC3SOFTWARELYS A:107 , PRO A:109 , LEU A:110 , THR A:112 , ASN A:122 , GLY A:325 , GLU A:340 , PRO A:341 , VAL A:342 , HIS A:343 , GLY A:344 , THR A:345 , ALA A:346 , TYR A:349 , ILE A:355 , ASN A:356 , ASP A:397 , ARG A:400BINDING SITE FOR RESIDUE NAP A 1001
4AC4SOFTWAREARG A:136 , ARG A:159 , TYR A:166 , ASP A:311 , CA A:1006 , HOH A:1136 , LYS B:233 , ASN B:235 , ASP B:287BINDING SITE FOR RESIDUE ICT A 1002
5AC5SOFTWAREASN A:235 , ILE A:285 , ASN A:288 , GLN A:291 , GLN A:292 , ARG A:296 , PRO B:109 , LEU B:110 , THR B:112 , ASN B:122 , ARG B:126 , ILE B:324 , GLY B:325 , GLU B:340 , VAL B:342 , HIS B:343 , GLY B:344 , THR B:345 , ALA B:346 , LYS B:348 , TYR B:349 , ILE B:355 , ASN B:356 , ASP B:397 , ICT B:1004 , HOH B:1008 , HOH B:1009 , HOH B:1010BINDING SITE FOR RESIDUE NAP B 1003
6AC6SOFTWARELYS A:233 , ASP A:287 , CA A:1005 , THR B:112 , SER B:120 , ASN B:122 , ARG B:126 , ARG B:136 , ARG B:159 , TYR B:166 , ASP B:311 , NAP B:1003 , HOH B:1005 , HOH B:1007BINDING SITE FOR RESIDUE ICT B 1004

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:87
2B:9 -B:87

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XKD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XKD)

(-) 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:427
 aligned with Q9YE81_AERPE | Q9YE81 from UniProtKB/TrEMBL  Length:432

    Alignment length:431
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431 
         Q9YE81_AERPE     2 ASPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESALKVVDAAVKKVYGGSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALKGPLETPVGTGYRSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVIFRENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRFATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFREHVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNLNGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINPSAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQPLRTSEYTETLIAYIDEADLNEVLAGKRG 432
               SCOP domains d1xkda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1xkdA00 A:5-435 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.........eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhh...hhhhhhhhhhhheeee.......----.hhhhhhhhhhh..eeeeee..........hhhhh.eeeeee..hhhhhh.ee...hhhhhhhhhhhhhhhh......eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh...eeehhhhhhh.........eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh.hhhh.eeeee....eeeee....hhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkd A   5 ASPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESALKVVDAAVKKVYGGSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALKGPLETPV----RSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVIFRENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRFATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFREHVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNLNGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINPSAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQPLRTSEYTETLIAYIDEADLNEVLAGKRG 435
                                    14        24        34        44        54        64        74        84        94       104       114    |  124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434 
                                                                                                                                       114  119                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:419
 aligned with Q9YE81_AERPE | Q9YE81 from UniProtKB/TrEMBL  Length:432

    Alignment length:421
                                    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       402       412       422 
         Q9YE81_AERPE     3 SPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESALKVVDAAVKKVYGGSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALKGPLETPVGTGYRSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVIFRENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRFATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFREHVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNLNGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINPSAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQPLRTSEYTETLIAYIDEADL 423
               SCOP domains d1xkdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1xkdB00 B:6-426 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------------------------------Iso_dh-1xkdB01 B:37-417                                                                                                                                                                                                                                                                                                                                                                      --------- Pfam domains (1)
           Pfam domains (2) -------------------------------Iso_dh-1xkdB02 B:37-417                                                                                                                                                                                                                                                                                                                                                                      --------- Pfam domains (2)
         Sec.struct. author ...............ee.eee..eee....eeeeee....hhhhhhhhhhhhhhhhh...--.....eeee...hhhhhhhh....hhhhhhhhhhhheeee............hhhhhhhhhh...eeeeee..........hhhhh.eeeeee..hhhhhh.ee...hhhhhhhhhhhhhhhh......eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh...eeehhhhh...........eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh.hhhhh..eeee..eeee......hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xkd B   6 SPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESALKVVDAAVKKV--GSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALKGPLETPVGTGYRSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVIFRENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRFATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFREHVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNLNGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINPSAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQPLRTSEYTETLIAYIDEADL 426
                                    15        25        35        45        55        65  |     75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425 
                                                                                      65 68
   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   (Q9YE81_AERPE | Q9YE81)
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
        Q9YE81_AERPE | Q9YE81: 1tyo 1v94 1xgv

(-) Related Entries Specified in the PDB File

1tyo ISOCITRATE DEHYDROGENASE FROM AEROPYRUM PERNIX IN COMPLEX WITH ETHENO-NADP
1xgv ISOCITRATE DEHYDROGENASE FROM AEROPYRUM PERNIX