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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi196 – 1961Zinc1 Publication
Metal bindingi198 – 1981Zinc1 Publication
Metal bindingi203 – 2031Zinc1 Publication
Metal bindingi245 – 2451Zinc1 Publication

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2782784-deoxy-L-threo-5-hexosulose-uronate ketol-isomerasePRO_0000215485Add
BLAST

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 interactions.
DIPiDIP-10069N.
IntActiQ46938. 2 interactions.
STRINGi511145.b2843.

Structurei

Secondary structure

1
278
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Helixi9 – 124Combined sources
Helixi17 – 248Combined sources
Beta strandi38 – 403Combined sources
Turni41 – 444Combined sources
Beta strandi45 – 517Combined sources
Beta strandi53 – 553Combined sources
Beta strandi57 – 604Combined sources
Helixi61 – 666Combined sources
Beta strandi69 – 713Combined sources
Turni72 – 754Combined sources
Beta strandi76 – 827Combined sources
Beta strandi87 – 915Combined sources
Beta strandi94 – 985Combined sources
Beta strandi103 – 1064Combined sources
Beta strandi113 – 1186Combined sources
Beta strandi126 – 1327Combined sources
Beta strandi140 – 1423Combined sources
Helixi144 – 1474Combined sources
Beta strandi150 – 1523Combined sources
Helixi155 – 1573Combined sources
Beta strandi161 – 1688Combined sources
Turni169 – 1713Combined sources
Beta strandi178 – 1847Combined sources
Beta strandi190 – 1923Combined sources
Beta strandi194 – 1974Combined sources
Beta strandi201 – 2099Combined sources
Beta strandi216 – 2227Combined sources
Beta strandi225 – 2317Combined sources
Beta strandi233 – 2397Combined sources
Beta strandi244 – 2518Combined sources
Beta strandi254 – 2629Combined sources
Beta strandi269 – 2724Combined sources
Helixi274 – 2774Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X8MX-ray2.60A/B/C/D/E/F2-278[»]
1XRUX-ray1.94A/B1-278[»]
ProteinModelPortaliQ46938.
SMRiQ46938. Positions 1-277.
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.
OrthoDBiEOG664CJZ.
PhylomeDBiQ46938.

Family and domain databases

Gene3Di2.60.120.500. 1 hit.
2.60.120.520. 1 hit.
HAMAPiMF_00687. KduI.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1X8MX-ray2.60A/B/C/D/E/F2-278[»]
1XRUX-ray1.94A/B1-278[»]
ProteinModelPortaliQ46938.
SMRiQ46938. Positions 1-277.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261944. 13 interactions.
DIPiDIP-10069N.
IntActiQ46938. 2 interactions.
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.
OrthoDBiEOG664CJZ.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Crystallization of 5-keto-4-deoxyuronate isomerase from Escherichia coli."
    Dunten P., Jaffe H., Aksamit R.R.
    Acta Crystallogr. D 54:678-680(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-20 AND 227-247, CRYSTALLIZATION, SUBUNIT.
  4. "Impact of nutritional factors on the proteome of intestinal Escherichia coli: induction of OxyR-dependent proteins AhpF and Dps by a lactose-rich diet."
    Rothe M., Alpert C., Engst W., Musiol S., Loh G., Blaut M.
    Appl. Environ. Microbiol. 78:3580-3591(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12.
  5. "Novel insights into E. coli's hexuronate metabolism: KduI facilitates the conversion of galacturonate and glucuronate under osmotic stress conditions."
    Rothe M., Alpert C., Loh G., Blaut M.
    PLoS ONE 8:E56906-E56906(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.
    Strain: K12 / MG1655 / ATCC 47076.
  6. "The crystal structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli."
    Fedorov A.A., Fedorov E.V., Almo S.C.
    Submitted (AUG-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS).
  7. "The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli."
    Crowther R.L., Georgiadis M.M.
    Proteins 61:680-684(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR, SUBUNIT.
    Strain: K12 / DH5-alpha.

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: January 20, 2016
This is version 122 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.