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Protein

3-isopropylmalate dehydratase small subunit

Gene

leuD

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate.By similarity

Catalytic activityi

(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate.

Pathwayi: L-leucine biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD)
  3. no protein annotated in this organism
  4. no protein annotated in this organism
This subpathway is part of the pathway L-leucine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate, the pathway L-leucine biosynthesis and in Amino-acid biosynthesis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Branched-chain amino acid biosynthesis, Leucine biosynthesis

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-1722-MONOMER.
BRENDAi4.2.1.33. 5244.
UniPathwayiUPA00048; UER00071.

Names & Taxonomyi

Protein namesi
Recommended name:
3-isopropylmalate dehydratase small subunit (EC:4.2.1.33)
Alternative name(s):
Alpha-IPM isomerase
Short name:
IPMI
Isopropylmalate isomerase
Gene namesi
Name:leuD
Ordered Locus Names:PH1724
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1631633-isopropylmalate dehydratase small subunitPRO_0000141949Add
BLAST

Interactioni

Subunit structurei

Heterodimer of LeuC and LeuD.By similarity

Protein-protein interaction databases

STRINGi70601.PH1724.

Structurei

Secondary structure

1
163
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 98Combined sources
Helixi16 – 194Combined sources
Helixi30 – 367Combined sources
Turni37 – 415Combined sources
Helixi45 – 484Combined sources
Beta strandi54 – 563Combined sources
Beta strandi59 – 613Combined sources
Helixi69 – 779Combined sources
Beta strandi81 – 855Combined sources
Helixi89 – 9810Combined sources
Beta strandi102 – 1054Combined sources
Beta strandi115 – 1195Combined sources
Turni120 – 1234Combined sources
Beta strandi124 – 1274Combined sources
Beta strandi130 – 1334Combined sources
Helixi139 – 1468Combined sources
Helixi150 – 1567Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V7LX-ray1.98A/B1-163[»]
ProteinModelPortaliO59393.
SMRiO59393. Positions 1-163.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO59393.

Family & Domainsi

Sequence similaritiesi

Belongs to the LeuD family. LeuD type 2 subfamily.Curated

Phylogenomic databases

eggNOGiarCOG02230. Archaea.
COG0066. LUCA.
HOGENOMiHOG000222940.
KOiK01704.
OMAiITPGRYN.

Family and domain databases

Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR011827. LeuD_type2/HacB/DmdB.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00694. Aconitase_C. 1 hit.
[Graphical view]
SUPFAMiSSF52016. SSF52016. 1 hit.
TIGRFAMsiTIGR02087. LEUD_arch. 1 hit.

Sequencei

Sequence statusi: Complete.

O59393-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITTGKVWKF GDDISTDEIT PGRYNLTKDP KELAKIAFIE VRPDFARNVR
60 70 80 90 100
PGDVVVAGKN FGIGSSRESA ALALKALGIA GVIAESFGRI FYRNAINIGI
110 120 130 140 150
PLLLGKTEGL KDGDLVTVNW ETGEVRKGDE ILMFEPLEDF LLEIVREGGI
160
LEYIRRRGDL CIR
Length:163
Mass (Da):18,011
Last modified:August 1, 1998 - v1
Checksum:iAEFBDDE1CBCDD266
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30838.1.
PIRiG71180.
RefSeqiWP_010885788.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA30838; BAA30838; BAA30838.
GeneIDi1442569.
KEGGipho:PH1724.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30838.1.
PIRiG71180.
RefSeqiWP_010885788.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V7LX-ray1.98A/B1-163[»]
ProteinModelPortaliO59393.
SMRiO59393. Positions 1-163.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH1724.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA30838; BAA30838; BAA30838.
GeneIDi1442569.
KEGGipho:PH1724.

Phylogenomic databases

eggNOGiarCOG02230. Archaea.
COG0066. LUCA.
HOGENOMiHOG000222940.
KOiK01704.
OMAiITPGRYN.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00071.
BioCyciPHOR70601:GJWR-1722-MONOMER.
BRENDAi4.2.1.33. 5244.

Miscellaneous databases

EvolutionaryTraceiO59393.

Family and domain databases

Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR011827. LeuD_type2/HacB/DmdB.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00694. Aconitase_C. 1 hit.
[Graphical view]
SUPFAMiSSF52016. SSF52016. 1 hit.
TIGRFAMsiTIGR02087. LEUD_arch. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

Entry informationi

Entry nameiLEUD_PYRHO
AccessioniPrimary (citable) accession number: O59393
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: July 6, 2016
This is version 106 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

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.