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Escherichia coli K-12 substr. MG1655 Enzyme: 2-keto-3-deoxygluconokinase



Gene: kdgK Accession Numbers: EG12253 (EcoCyc), b3526, ECK3511

Synonyms: yhjI

Regulation Summary Diagram: ?

Summary:
2-keto-3-deoxygluconokinase catalyzes the ATP-dependent phosphorylation of the first common intermediate in the D-glucuronate and D-galacturonate degradation pathways, 2-dehydro-3-deoxy-D-gluconate [Cynkin60, Pouyssegur74].

The activity of KdgK increases 5-fold in cells grown on galacturonate or glucoronate rather than on glucose [Cynkin60, Pouyssegur71].

KdgK: "2-keto-3-deoxygluconokinase" [Pouyssegur72]

Gene Citations: [Plunkett93, Blattner97]

Locations: cytosol

Map Position: [3,677,442 -> 3,678,371] (79.26 centisomes)
Length: 930 bp / 309 aa

Molecular Weight of Polypeptide: 33.962 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011519 , CGSC:591 , DIP:DIP-10056N , EchoBASE:EB2163 , EcoGene:EG12253 , EcoliWiki:b3526 , Mint:MINT-1219186 , ModBase:P37647 , OU-Microarray:b3526 , PortEco:kdgK , PR:PRO_000023047 , Pride:P37647 , Protein Model Portal:P37647 , RefSeq:NP_417983 , RegulonDB:EG12253 , SMR:P37647 , String:511145.b3526 , UniProt:P37647

Relationship Links: InterPro:IN-FAMILY:IPR002173 , InterPro:IN-FAMILY:IPR011611 , Pfam:IN-FAMILY:PF00294 , Prosite:IN-FAMILY:PS00583 , Prosite:IN-FAMILY:PS00584

In Paralogous Gene Group: 340 (11 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0019698 - D-galacturonate catabolic process Inferred from experiment [Pouyssegur74, Pouyssegur71]
GO:0042840 - D-glucuronate catabolic process Inferred from experiment [Pouyssegur74, Pouyssegur71]
GO:0046835 - carbohydrate phosphorylation Inferred by computational analysis Inferred from experiment [Pouyssegur71, GOA01a]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008673 - 2-dehydro-3-deoxygluconokinase activity Inferred from experiment Inferred by computational analysis [GOA01a, Pouyssegur71]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016773 - phosphotransferase activity, alcohol group as acceptor Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for kdgK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Curated 21-Sep-2006 by Shearer A , SRI International
Last-Curated ? 01-Feb-2008 by Keseler I , SRI International


Enzymatic reaction of: 2-keto-3-deoxygluconokinase

Synonyms: ketodeoxygluconokinase, ATP:2-dehydro-3-deoxy-D-gluconate 6-phosphotransferase, 3-deoxy-2-oxo-D-gluconate kinase, KDG kinase

2-dehydro-3-deoxy-D-gluconate + ATP <=> 2-dehydro-3-deoxy-D-gluconate 6-phosphate + ADP + H+

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

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of hexuronide and hexuronate degradation , superpathway of β-D-glucuronide and D-glucuronate degradation , D-galacturonate degradation I , D-fructuronate degradation

Summary:
Although the enzyme is most active with Mn2+ as a cofactor, it can also operate with Mg2+ or Co2+ [Cynkin60, Pouyssegur71].

Cofactors or Prosthetic Groups: Mn2+ [Pouyssegur71, Cynkin60]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
1000.0, 1000.0
[Pouyssegur71]
2-dehydro-3-deoxy-D-gluconate
1000.0, 1000.0
[Pouyssegur71]

pH(opt): 6 [BRENDA14, Pouyssegur71], 6-6.5 [Pouyssegur71]


Sequence Features

Feature Class Location Attached Group Citations Comment
Amino-Acid-Sites-That-Bind 88  
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Protein-Segment 102 -> 104  
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Nucleotide-Phosphate-Binding-Region 168 -> 170 ATP
[UniProt14]
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 170  
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 197  
[UniProt13]
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Nucleotide-Phosphate-Binding-Region 228 -> 234 ATP
[UniProt14]
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Nucleotide-Phosphate-Binding-Region 261 -> 264 ATP
[UniProt14]
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 264  
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Active-Site 264  
[UniProt13]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3526 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12253; confirmed by SwissProt match.


References

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

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Cynkin60: Cynkin MA, Ashwell G (1960). "Uronic acid metabolism in bacteria. IV. Purification and properties of 2-keto-3-deoxy-D-gluconokinase in Escherichia coli." J Biol Chem 235;1576-9. PMID: 13813474

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Pouyssegur71: Pouyssegur J, Stoeber F (1971). "[Study of the common degradative pathway of hexuronates in Escherichia coli K 12. Purification, properties and individuality of 2-keto-3-deoxy-D-gluconnokinase]." Biochimie 53(6);771-81. PMID: 4944816

Pouyssegur72: Pouyssegur JM, Stoeber FR (1972). "[A common pathway for hexouronate degradation in Escherichia coli K 12. Induction mechanism of 2-keto-3-deoxy-gluconate metabolizing enzymes]." Eur J Biochem 30(3);479-94. PMID: 4565407

Pouyssegur74: Pouyssegur J, Stoeber F (1974). "Genetic control of the 2-keto-3-deoxy-d-gluconate metabolism in Escherichia coli K-12: kdg regulon." J Bacteriol 117(2);641-51. PMID: 4359651

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
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 18.5 on Thu Dec 18, 2014, BIOCYC14B.