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O29610

- IDH_ARCFU

UniProt

O29610 - IDH_ARCFU

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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Binds 1 magnesium or manganese ion per subunit.By similarity

Kineticsi

  1. KM=118 µM for D,L-isocitrate
  2. KM=30 µM for NADP
  3. KM=5.4 mM for NAD

Vmax=141 µmol/min/mg enzyme towards NADP at 60 degrees Celsius

Vmax=14.5 µmol/min/mg enzyme towards NAD

pH dependencei

Optimum pH is 8.6.

Temperature dependencei

Optimum temperature is 90 degrees Celsius. Thermostable.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei100 – 1001NADPBy similarity
Binding sitei109 – 1091SubstrateBy similarity
Binding sitei111 – 1111SubstrateBy similarity
Binding sitei115 – 1151SubstrateBy similarity
Binding sitei125 – 1251SubstrateBy similarity
Binding sitei149 – 1491SubstrateBy similarity
Sitei156 – 1561Critical for catalysisBy similarity
Sitei223 – 2231Critical for catalysisBy similarity
Metal bindingi301 – 3011Magnesium or manganeseBy similarity
Binding sitei346 – 3461NADP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei385 – 3851NADPBy similarity
Binding sitei389 – 3891NADPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi333 – 3397NADPBy similarity

GO - Molecular functioni

  1. isocitrate dehydrogenase (NADP+) activity Source: UniProtKB-EC
  2. magnesium ion binding Source: InterPro
  3. NAD binding Source: InterPro

GO - Biological processi

  1. glyoxylate cycle Source: UniProtKB-KW
  2. tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-662-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:icd
Ordered Locus Names:AF_0647
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
ProteomesiUP000002199: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 412412Isocitrate dehydrogenase [NADP]PRO_0000083572Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei109 – 1091PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi224325.AF0647.

Structurei

Secondary structure

1
412
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 183
Beta strandi21 – 233
Beta strandi26 – 338
Helixi39 – 5719
Beta strandi62 – 654
Helixi70 – 767
Helixi82 – 9110
Beta strandi93 – 964
Beta strandi103 – 1086
Helixi109 – 1179
Beta strandi122 – 1287
Beta strandi136 – 1383
Helixi140 – 1423
Beta strandi144 – 1507
Beta strandi152 – 1543
Helixi155 – 1573
Helixi166 – 17914
Beta strandi187 – 1959
Helixi196 – 21217
Beta strandi216 – 2227
Turni224 – 2263
Turni228 – 2303
Helixi231 – 24515
Turni247 – 2493
Helixi253 – 2608
Beta strandi269 – 2757
Helixi276 – 2783
Helixi279 – 2857
Helixi287 – 2893
Beta strandi292 – 2954
Helixi297 – 31014
Helixi314 – 3163
Beta strandi318 – 3236
Beta strandi326 – 3338
Turni338 – 3414
Helixi348 – 36013
Helixi364 – 37916
Helixi385 – 3917
Beta strandi393 – 3953
Helixi398 – 41114

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2IV0X-ray2.50A/B1-412[»]
ProteinModelPortaliO29610.
SMRiO29610. Positions 1-412.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29610.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
KOiK00031.
OMAiCLRPIRY.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00183. prok_nadp_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29610-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQYEKVKPPE NGEKIRYENG KLIVPDNPII PYFEGDGIGK DVVPAAIRVL
60 70 80 90 100
DAAADKIGKE VVWFQVYAGE DAYKLYGNYL PDDTLNAIKE FRVALKGPLT
110 120 130 140 150
TPVGGGYRSL NVTIRQVLDL YANVRPVYYL KGVPSPIKHP EKVNFVIFRE
160 170 180 190 200
NTEDVYAGIE WPRGSEEALK LIRFLKNEFG VTIREDSGIG IKPISEFATK
210 220 230 240 250
RLVRMAIRYA IENNRKSVTL VHKGNIMKYT EGAFRDWGYE VAKQEFGEYC
260 270 280 290 300
ITEDELWDKY GGKQPEGKIV VKDRIADNMF QQILTRTDEY DVIALPNLNG
310 320 330 340 350
DYLSDAAAAL IGGLGIAPGS NIGDGIGVFE PVHGSAPKYA GQNKVNPTAE
360 370 380 390 400
ILTGALMFEY IGWKDASEMI KKAVEMTISS GIVTYDIHRH MGGTKVGTRE
410
FAEAVVENLQ SL
Length:412
Mass (Da):45,842
Last modified:January 1, 1998 - v1
Checksum:iA2E1A3AA7662D3EA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z96105 Genomic DNA. Translation: CAB09535.1.
AE000782 Genomic DNA. Translation: AAB90591.1.
PIRiG69330.
RefSeqiNP_069481.1. NC_000917.1.
WP_010878150.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90591; AAB90591; AF_0647.
GeneIDi1483865.
KEGGiafu:AF0647.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z96105 Genomic DNA. Translation: CAB09535.1 .
AE000782 Genomic DNA. Translation: AAB90591.1 .
PIRi G69330.
RefSeqi NP_069481.1. NC_000917.1.
WP_010878150.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2IV0 X-ray 2.50 A/B 1-412 [» ]
ProteinModelPortali O29610.
SMRi O29610. Positions 1-412.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224325.AF0647.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAB90591 ; AAB90591 ; AF_0647 .
GeneIDi 1483865.
KEGGi afu:AF0647.

Phylogenomic databases

eggNOGi COG0538.
KOi K00031.
OMAi CLRPIRY.

Enzyme and pathway databases

BioCyci AFUL224325:GJBC-662-MONOMER.

Miscellaneous databases

EvolutionaryTracei O29610.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11835. PTHR11835. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00183. prok_nadp_idh. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus."
    Steen I.H., Lien T., Birkeland N.-K.
    Arch. Microbiol. 168:412-420(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-27, CHARACTERIZATION.
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

Entry informationi

Entry nameiIDH_ARCFU
AccessioniPrimary (citable) accession number: O29610
Secondary accession number(s): O31221
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 29, 2001
Last sequence update: January 1, 1998
Last modified: October 1, 2014
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3