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(-) Description

Title :  ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED)
 
Authors :  S. A. Doyle, P. T. Beernink, D. E. Koshland Junior
Date :  08 Jan 01  (Deposition) - 16 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Oxidoreductase (Nad(A)-Choh(D)), Nadp, Phosphorylation, Glyoxylate Bypass (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Doyle, P. T. Beernink, D. E. Koshland Junior
Structural Basis For A Change In Substrate Specificity: Crystal Structure Of S113E Isocitrate Dehydrogenase In A Complex With Isopropylmalate, Mg2+ And Nadp
Biochemistry V. 40 4234 2001
PubMed-ID: 11284679  |  Reference-DOI: 10.1021/BI002533Q

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: ICD
    Expression System Plasmid: PTK513
    Expression System Strain: JLK1
    Expression System Taxid: 562
    Expression System Vector: PUC
    Expression System Vector Type: PLASMID
    Gene: ICD
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Plasmid: PTK513
    Synonym: OXALOSUCCINATE DECARBOXYLASE, IDH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IPM1Ligand/Ion3-ISOPROPYLMALIC ACID
3MG1Ligand/IonMAGNESIUM ION
4NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IPM2Ligand/Ion3-ISOPROPYLMALIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:283 , ASP A:307 , IPM A:1419 , HOH A:2187 , HOH A:2201BINDING SITE FOR RESIDUE MG A1421
2AC2SOFTWAREGLU A:113 , ARG A:119 , ARG A:129 , ARG A:153 , TYR A:160 , LYS A:230 , ILE A:233 , ASP A:283 , ASP A:307 , NAP A:1420 , MG A:1421 , HOH A:2226BINDING SITE FOR RESIDUE IPM A1419
3AC3SOFTWAREGLU A:60 , LYS A:100 , PRO A:102 , LEU A:103 , THR A:104 , ASN A:115 , GLN A:288 , ARG A:292 , ILE A:320 , GLY A:321 , GLU A:336 , THR A:338 , HIS A:339 , GLY A:340 , THR A:341 , ALA A:342 , TYR A:345 , VAL A:351 , ASN A:352 , TYR A:391 , ASP A:392 , IPM A:1419 , HOH A:2227 , HOH A:2228 , HOH A:2230 , HOH A:2232BINDING SITE FOR RESIDUE NAP A1420
4AC4SOFTWAREARG A:96 , ILE A:328 , GLY A:329 , ASP A:330 , CYS A:332 , ALA A:333 , HIS A:366 , GOL A:1418BINDING SITE FOR RESIDUE GOL A1417
5AC5SOFTWAREPHE A:152 , HIS A:366 , GOL A:1417 , HOH A:2142 , HOH A:2206BINDING SITE FOR RESIDUE GOL A1418

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HJ6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:261 -Pro A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HJ6)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDH_ECOLI303-322  1A:303-322
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDH_ECOLI303-322  2A:303-322

(-) Exons   (0, 0)

(no "Exon" information available for 1HJ6)

(-) 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:414
 aligned with IDH_ECOLI | P08200 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:414
                                    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    
            IDH_ECOLI     3 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
               SCOP domains d1hj6a_ A: Isocitrate dehydrogenase, ICDH                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1hj6A00 A:3-416 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhh.....hhhhhhhhhhhheeee............hhhhhhhhhh...eeeeeee..........hhhh.eeeeeee..hhhhhh......hhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh.........eeee......eeeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee....eeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hj6 A   3 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRELNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
                                    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
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HJ6)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (IDH_ECOLI | P08200)
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: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:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDH_ECOLI | P08200: 1ai2 1ai3 1bl5 1cw1 1cw4 1cw7 1gro 1grp 1idc 1idd 1ide 1idf 1ika 1iso 1p8f 1pb1 1pb3 1sjs 3icd 3lcb 4aj3 4aja 4ajb 4ajc 4ajr 4ajs 4bnp 4icd 4p69 5icd 6icd 7icd 8icd 9icd

(-) Related Entries Specified in the PDB File

1ai2 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED)
1ai3 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES
1bl5 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION
1cw1 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO ISOCITRATE AND MN2+
1cw4 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA- KETOGLUTARATE
1cw7 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOCITRATE
1gro MOL_ID: 1; MOLECULE: ISOCITRATE DEHYDROGENASE; CHAIN: NULL; EC: 1.1.1.42; ENGINEERED: YES; MUTATION: S113E, N115L
1grp MOL_ID: 1; MOLECULE: ISOCITRATE DEHYDROGENASE; CHAIN: NULL; EC: 1.1.1.42; MUTATION: N115L
1idc ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY
1idd ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME
1ide ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION)
1idf ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME
1iso ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP+ --> NAD+ SPECIFICITY-REVERSAL MUTANT
1sjs ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY DOMAIN SHIFTING