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Protein

4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

Gene

kduI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the isomerization of 5-dehydro-4-deoxy-D-glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate (By similarity). Plays a role in the catabolism of hexuronates under osmotic stress conditions, likely substituting for the regular hexuronate degrading enzyme UxaC whose expression is repressed in these conditions (PubMed:23437267).By similarity1 Publication

Catalytic activityi

5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate.

Cofactori

Zn2+Curated1 PublicationNote: Binds 1 zinc ion per subunit. The bound metal seen in the crystal structure was tentatively identified as zinc, and its requirement for activity has not been shown.Curated1 Publication

Pathwayi: pectin degradation

This protein is involved in step 4 of the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (kduI)
  5. no protein annotated in this organism
This subpathway is part of the pathway pectin degradation, which is itself part of Glycan metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin, the pathway pectin degradation and in Glycan metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi196Zinc1 Publication1
Metal bindingi198Zinc1 Publication1
Metal bindingi203Zinc1 Publication1
Metal bindingi245Zinc1 Publication1

GO - Molecular functioni

  • 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • metal ion binding Source: EcoCyc
  • zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • D-galacturonate catabolic process Source: EcoCyc
  • D-glucuronate catabolic process Source: EcoCyc
  • pectin catabolic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G7463-MONOMER.
ECOL316407:JW2811-MONOMER.
MetaCyc:G7463-MONOMER.
BRENDAi5.3.1.17. 2026.
UniPathwayiUPA00545; UER00826.

Names & Taxonomyi

Protein namesi
Recommended name:
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (EC:5.3.1.17)
Alternative name(s):
5-keto-4-deoxyuronate isomerase
DKI isomerase
Gene namesi
Name:kduI
Synonyms:yqeE
Ordered Locus Names:b2843, JW2811
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13096. kduI.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002154851 – 2784-deoxy-L-threo-5-hexosulose-uronate ketol-isomeraseAdd BLAST278

Proteomic databases

PaxDbiQ46938.
PRIDEiQ46938.

Expressioni

Inductioni

Its expression is up-regulated in the presence of galacturonate and glucuronate (PubMed:23437267). Is also down-regulated in E.coli of mice fed a casein-rich diet (PubMed:22427493).2 Publications

Interactioni

Subunit structurei

Homohexamer.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261944. 13 interactors.
DIPiDIP-10069N.
IntActiQ46938. 2 interactors.
STRINGi511145.b2843.

Structurei

Secondary structure

1278
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Helixi9 – 12Combined sources4
Helixi17 – 24Combined sources8
Beta strandi38 – 40Combined sources3
Turni41 – 44Combined sources4
Beta strandi45 – 51Combined sources7
Beta strandi53 – 55Combined sources3
Beta strandi57 – 60Combined sources4
Helixi61 – 66Combined sources6
Beta strandi69 – 71Combined sources3
Turni72 – 75Combined sources4
Beta strandi76 – 82Combined sources7
Beta strandi87 – 91Combined sources5
Beta strandi94 – 98Combined sources5
Beta strandi103 – 106Combined sources4
Beta strandi113 – 118Combined sources6
Beta strandi126 – 132Combined sources7
Beta strandi140 – 142Combined sources3
Helixi144 – 147Combined sources4
Beta strandi150 – 152Combined sources3
Helixi155 – 157Combined sources3
Beta strandi161 – 168Combined sources8
Turni169 – 171Combined sources3
Beta strandi178 – 184Combined sources7
Beta strandi190 – 192Combined sources3
Beta strandi194 – 197Combined sources4
Beta strandi201 – 209Combined sources9
Beta strandi216 – 222Combined sources7
Beta strandi225 – 231Combined sources7
Beta strandi233 – 239Combined sources7
Beta strandi244 – 251Combined sources8
Beta strandi254 – 262Combined sources9
Beta strandi269 – 272Combined sources4
Helixi274 – 277Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X8MX-ray2.60A/B/C/D/E/F2-278[»]
1XRUX-ray1.94A/B1-278[»]
ProteinModelPortaliQ46938.
SMRiQ46938.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46938.

Family & Domainsi

Sequence similaritiesi

Belongs to the KduI family.Curated

Phylogenomic databases

eggNOGiENOG4105D50. Bacteria.
COG3717. LUCA.
HOGENOMiHOG000124379.
InParanoidiQ46938.
KOiK01815.
OMAiIWAMAGE.
PhylomeDBiQ46938.

Family and domain databases

Gene3Di2.60.120.500. 1 hit.
2.60.120.520. 1 hit.
HAMAPiMF_00687. KduI. 1 hit.
InterProiIPR007045. KduI.
IPR021120. KduI/IolB_isomerase.
IPR027447. KduI_C.
IPR027449. KduI_N.
IPR011051. RmlC_Cupin.
[Graphical view]
PfamiPF04962. KduI. 1 hit.
[Graphical view]
PIRSFiPIRSF006625. KduI. 1 hit.
SUPFAMiSSF51182. SSF51182. 1 hit.

Sequencei

Sequence statusi: Complete.

Q46938-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVRQSIHSA HAKTLDTQGL RNEFLVEKVF VADEYTMVYS HIDRIIVGGI
60 70 80 90 100
MPITKTVSVG GEVGKQLGVS YFLERRELGV INIGGAGTIT VDGQCYEIGH
110 120 130 140 150
RDALYVGKGA KEVVFASIDT GTPAKFYYNC APAHTTYPTK KVTPDEVSPV
160 170 180 190 200
TLGDNLTSNR RTINKYFVPD VLETCQLSMG LTELAPGNLW NTMPCHTHER
210 220 230 240 250
RMEVYFYFNM DDDACVFHMM GQPQETRHIV MHNEQAVISP SWSIHSGVGT
260 270
KAYTFIWGMV GENQVFDDMD HVAVKDLR
Length:278
Mass (Da):31,076
Last modified:November 1, 1996 - v1
Checksum:iF7CD5C259503CD1A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40490.1.
U00096 Genomic DNA. Translation: AAC75882.1.
AP009048 Genomic DNA. Translation: BAE76912.1.
PIRiD65067.
RefSeqiNP_417320.1. NC_000913.3.
WP_000383237.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75882; AAC75882; b2843.
BAE76912; BAE76912; BAE76912.
GeneIDi947319.
KEGGiecj:JW2811.
eco:b2843.
PATRICi32121104. VBIEscCol129921_2941.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40490.1.
U00096 Genomic DNA. Translation: AAC75882.1.
AP009048 Genomic DNA. Translation: BAE76912.1.
PIRiD65067.
RefSeqiNP_417320.1. NC_000913.3.
WP_000383237.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X8MX-ray2.60A/B/C/D/E/F2-278[»]
1XRUX-ray1.94A/B1-278[»]
ProteinModelPortaliQ46938.
SMRiQ46938.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261944. 13 interactors.
DIPiDIP-10069N.
IntActiQ46938. 2 interactors.
STRINGi511145.b2843.

Proteomic databases

PaxDbiQ46938.
PRIDEiQ46938.

Protocols and materials databases

DNASUi947319.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75882; AAC75882; b2843.
BAE76912; BAE76912; BAE76912.
GeneIDi947319.
KEGGiecj:JW2811.
eco:b2843.
PATRICi32121104. VBIEscCol129921_2941.

Organism-specific databases

EchoBASEiEB2899.
EcoGeneiEG13096. kduI.

Phylogenomic databases

eggNOGiENOG4105D50. Bacteria.
COG3717. LUCA.
HOGENOMiHOG000124379.
InParanoidiQ46938.
KOiK01815.
OMAiIWAMAGE.
PhylomeDBiQ46938.

Enzyme and pathway databases

UniPathwayiUPA00545; UER00826.
BioCyciEcoCyc:G7463-MONOMER.
ECOL316407:JW2811-MONOMER.
MetaCyc:G7463-MONOMER.
BRENDAi5.3.1.17. 2026.

Miscellaneous databases

EvolutionaryTraceiQ46938.
PROiQ46938.

Family and domain databases

Gene3Di2.60.120.500. 1 hit.
2.60.120.520. 1 hit.
HAMAPiMF_00687. KduI. 1 hit.
InterProiIPR007045. KduI.
IPR021120. KduI/IolB_isomerase.
IPR027447. KduI_C.
IPR027449. KduI_N.
IPR011051. RmlC_Cupin.
[Graphical view]
PfamiPF04962. KduI. 1 hit.
[Graphical view]
PIRSFiPIRSF006625. KduI. 1 hit.
SUPFAMiSSF51182. SSF51182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiKDUI_ECOLI
AccessioniPrimary (citable) accession number: Q46938
Secondary accession number(s): Q2M9Z4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 125 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.