Escherichia coli K-12 substr. MG1655 Enzyme: 5-dehydro-4-deoxy-D-glucuronate isomerase

Gene: kduI Accession Numbers: G7463 (EcoCyc), b2843, ECK2841

Synonyms: yqeE

Regulation Summary Diagram: ?

Regulation summary diagram for kduI

Subunit composition of 5-dehydro-4-deoxy-D-glucuronate isomerase = [KduI]6
         predicted 5-keto 4-deoxyuronate isomerase monomer = KduI

KduI was a predicted 5-keto 4-deoxyuronate isomerase due to its high sequence similarity to the enzyme from Erwinia chrysanthemi. In unpurified form, the enzyme appeares to be able to utilize both glucuronate and galacturonate, perhaps catalyzing the same reaction as UxaC. While UxaC expression is repressed under osmotic stress conditions, KduI expression appears to be unaffected, and it could therefore substitute for UxaC [Rothe13]. The purified protein was recently shown to catalyze the activity of EC, 5-dehydro-4-deoxy-D-glucuronate isomerase in coupled assays with KduD from Pectobacterium carotovorum or Streptococcus agalactiae [Maruyama15].

Crystal structures of KduI have been solved [Dunten98, Crowther05]. The enzyme binds a metal ion tentatively identified as Zn2+ and is structurally similar to members of the cupin superfamily of proteins [Crowther05]. In vivo homomultimeric KduI interaction can be detected in cross-linking experiments [Zheng11].

KduI was identified as a protein whose expression is 8-fold lower in E. coli found in the cecum of mice that were fed a casein diet compared to mice fed a starch diet [Rothe12]. Expression of kduI is increased in the presence of galacturonate and glucuronate [Rothe13].

Locations: cytosol

Map Position: [2,981,310 <- 2,982,146] (64.26 centisomes, 231°)
Length: 837 bp / 278 aa

Molecular Weight of Polypeptide: 31.076 kD (from nucleotide sequence), 33.0 kD (experimental) [Dunten98 ]

Molecular Weight of Multimer: 165.0 kD (experimental) [Crowther05]

Unification Links: ASAP:ABE-0009332 , DIP:DIP-10069N , EchoBASE:EB2899 , EcoGene:EG13096 , EcoliWiki:b2843 , ModBase:Q46938 , OU-Microarray:b2843 , PortEco:kduI , PR:PRO_000023059 , Pride:Q46938 , Protein Model Portal:Q46938 , RefSeq:NP_417320 , RegulonDB:G7463 , SMR:Q46938 , String:511145.b2843 , Swiss-Model:Q46938 , UniProt:Q46938

Relationship Links: InterPro:IN-FAMILY:IPR007045 , InterPro:IN-FAMILY:IPR011051 , InterPro:IN-FAMILY:IPR021120 , InterPro:IN-FAMILY:IPR027447 , InterPro:IN-FAMILY:IPR027449 , Panther:IN-FAMILY:PTHR30025:SF0 , PDB:Structure:1X8M , PDB:Structure:1XRU , Pfam:IN-FAMILY:PF04962

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0019698 - D-galacturonate catabolic process Inferred from experiment [Rothe13]
GO:0042840 - D-glucuronate catabolic process Inferred from experiment [Rothe13]
GO:0045490 - pectin catabolic process Inferred by computational analysis [UniProtGOA12, GOA06, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rodina11]
GO:0008697 - 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Maruyama15]
GO:0042802 - identical protein binding Inferred from experiment [Crowther05]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Crowther05]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016861 - intramolecular oxidoreductase activity, interconverting aldoses and ketoses Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Lasserre06]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for kduI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Imported from MetaCyc 04-Dec-2011 by Caspi R , SRI International
Last-Curated ? 05-Mar-2013 by Keseler I , SRI International

Enzymatic reaction of: 5-dehydro-4-deoxy-D-glucuronate isomerase

EC Number:

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

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Imported from MetaCyc 16-Mar-2015 by Caspi R , SRI International

Sequence Features

Protein sequence of predicted 5-keto 4-deoxyuronate isomerase monomer with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 196
[Crowther05, UniProt12a]
UniProt: Zinc.
Metal-Binding-Site 198
[Crowther05, UniProt12a]
UniProt: Zinc.
Metal-Binding-Site 203
[Crowther05, UniProt12a]
UniProt: Zinc.
Metal-Binding-Site 245
[Crowther05, UniProt12a]
UniProt: Zinc.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Crowther05: Crowther RL, Georgiadis MM (2005). "The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli." Proteins 61(3);680-4. PMID: 16152643

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dunten98: Dunten P, Jaffe H, Aksamit RR (1998). "Crystallization of 5-keto-4-deoxyuronate isomerase from Escherichia coli." Acta Crystallogr D Biol Crystallogr 54 ( Pt 4);678-80. PMID: 9761873

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Maruyama15: Maruyama Y, Oiki S, Takase R, Mikami B, Murata K, Hashimoto W (2015). "Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: Molecular identification and structure determination of streptococcal isomerase and dehydrogenase." J Biol Chem 290(10);6281-92. PMID: 25605731

Rodina11: Rodina E, Vorobieva N, Kurilova S, Mikulovich J, Vainonen J, Aro EM, Nazarova T (2011). "Identification of new protein complexes of Escherichia coli inorganic pyrophosphatase using pull-down assay." Biochimie 93(9);1576-83. PMID: 21664227

Rothe12: Rothe M, Alpert C, Engst W, Musiol S, Loh G, Blaut M (2012). "Impact of nutritional factors on the proteome of intestinal Escherichia coli: induction of OxyR-dependent proteins AhpF and Dps by a lactose-rich diet." Appl Environ Microbiol 78(10);3580-91. PMID: 22427493

Rothe13: Rothe M, Alpert C, Loh G, Blaut M (2013). "Novel Insights into E. coli's Hexuronate Metabolism: KduI Facilitates the Conversion of Galacturonate and Glucuronate under Osmotic Stress Conditions." PLoS One 8(2);e56906. PMID: 23437267

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Zheng11: Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011). "Cross-linking measurements of in vivo protein complex topologies." Mol Cell Proteomics 10(10);M110.006841. PMID: 21697552

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sun Oct 4, 2015, BIOCYC14B.