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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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001419491 – 1633-isopropylmalate dehydratase small subunitAdd BLAST163

Interactioni

Subunit structurei

Heterodimer of LeuC and LeuD.By similarity

Protein-protein interaction databases

STRINGi70601.PH1724.

Structurei

Secondary structure

1163
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 9Combined sources8
Helixi16 – 19Combined sources4
Helixi30 – 36Combined sources7
Turni37 – 41Combined sources5
Helixi45 – 48Combined sources4
Beta strandi54 – 56Combined sources3
Beta strandi59 – 61Combined sources3
Helixi69 – 77Combined sources9
Beta strandi81 – 85Combined sources5
Helixi89 – 98Combined sources10
Beta strandi102 – 105Combined sources4
Beta strandi115 – 119Combined sources5
Turni120 – 123Combined sources4
Beta strandi124 – 127Combined sources4
Beta strandi130 – 133Combined sources4
Helixi139 – 146Combined sources8
Helixi150 – 156Combined sources7

3D structure databases

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

CDDicd01577. IPMI_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2. 1 hit.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR033940. IPMI_Swivel.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V7LX-ray1.98A/B1-163[»]
ProteinModelPortaliO59393.
SMRiO59393.
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.
BRENDAi4.2.1.33. 5244.

Miscellaneous databases

EvolutionaryTraceiO59393.

Family and domain databases

CDDicd01577. IPMI_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2. 1 hit.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR033940. IPMI_Swivel.
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...

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: November 30, 2016
This is version 109 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.