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Escherichia coli K-12 substr. MG1655 Enzyme: 3-keto-L-gulonate 6-phosphate decarboxylase



Gene: ulaD Accession Numbers: G7858 (EcoCyc), b4196, ECK4192

Synonyms: yjfV, sgaH

Regulation Summary Diagram: ?

Subunit composition of 3-keto-L-gulonate 6-phosphate decarboxylase = [UlaD]2
         3-keto-L-gulonate 6-phosphate decarboxylase = UlaD

Summary:
3-keto-L-gulonate 6-phosphate decarboxylase is an enzyme in the pathway of anaerobic L-ascorbate degradation.

Crystal structures of the UlaD protein [Wise02], UlaD complexed with substrate, reaction intermediate and product analogs [Wise03], and several mutants [Wise04, Wise05] have been determined. The enzyme is as a dimer of antiparallel (β/α)8 barrels in the crystal structure [Wise02]. Active site residues and catalytic mechanisms involving a Mg2+ ion-stabilized cis-1,2-enediolate intermediate have been studied [Wise02, Wise03, Yew04, Wise04].

Kinetic properties of active site mutants have been analyzed [Yew04]. Certain changes to active site residues can enhance the D-arabino-hex-3-ulose 6-phosphate synthase (HPS) activity of the enzyme [Yew05]. The structural basis of the effect on the catalytic properties of the enzyme has been explored [Wise05].

UlaD: "utilization of L-ascorbate" [Yew02]

Gene Citations: [Campos02]

Locations: cytosol

Map Position: [4,420,209 -> 4,420,859] (95.27 centisomes)
Length: 651 bp / 216 aa

Molecular Weight of Polypeptide: 23.578 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013729 , DIP:DIP-10869N , EchoBASE:EB2389 , EcoGene:EG12496 , EcoliWiki:B4196 , ModBase:P39304 , OU-Microarray:b4196 , PortEco:ulaD , PR:PRO_000024178 , Pride:P39304 , Protein Model Portal:P39304 , RefSeq:NP_418617 , RegulonDB:G7858 , SMR:P39304 , String:511145.b4196 , UniProt:P39304

Relationship Links: InterPro:IN-FAMILY:IPR001754 , InterPro:IN-FAMILY:IPR011060 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR023942 , PDB:Structure:1KV8 , PDB:Structure:1KW1 , PDB:Structure:1Q6L , PDB:Structure:1Q6O , PDB:Structure:1Q6Q , PDB:Structure:1Q6R , PDB:Structure:1SO3 , PDB:Structure:1SO4 , PDB:Structure:1SO5 , PDB:Structure:1SO6 , PDB:Structure:1XBV , PDB:Structure:1XBX , PDB:Structure:1XBY , PDB:Structure:1XBZ , Pfam:IN-FAMILY:PF00215 , Smart:IN-FAMILY:SM00934

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019854 - L-ascorbic acid catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, GOA01a, Campos04]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006207 - 'de novo' pyrimidine nucleobase biosynthetic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Wise02]
GO:0033982 - 3-dehydro-L-gulonate-6-phosphate decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Yew02]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004590 - orotidine-5'-phosphate decarboxylase activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for ulaD 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:
Created 10-Nov-2008 by Keseler I , SRI International
Last-Curated ? 10-Nov-2008 by Keseler I , SRI International


Enzymatic reaction of: 3-keto-L-gulonate 6-phosphate decarboxylase

Synonyms: KGPDC

EC Number: 4.1.1.85

3-keto-L-gulonate 6-phosphate + H+ <=> L-xylulose -5-phosphate + CO2

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: L-ascorbate degradation I (bacterial, anaerobic)

Summary:
3-keto-L-gulonate is not a substrate [Yew02]. The enzyme can catalyze an aldol condensation reaction with D-ribulose 5-phosphate and L-xylulose 5-phosphate at low efficiency [Yew05].

Cofactors or Prosthetic Groups: Mg2+ [Wise02]

Kinetic Parameters:

Substrate
Km (μM)
Citations
3-keto-L-gulonate 6-phosphate
670.0
[Yew04]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 11
[UniProt10]
UniProt: Substrate;
Mutagenesis-Variant 33
[Yew04, UniProt11]
Alternate sequence: E → K; UniProt: Loss of activity.
Metal-Binding-Site 33
[UniProt10]
UniProt: Magnesium;
Metal-Binding-Site 62
[UniProt10]
UniProt: Magnesium;
Mutagenesis-Variant 64
[Yew04, UniProt11]
Alternate sequence: K → A; UniProt: 16% of wild-type activity.
Amino-Acid-Site 64
[UniProt10]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;
Mutagenesis-Variant 67
[Yew04, UniProt11]
Alternate sequence: D → A; UniProt: 5% of wild-type activity.
Amino-Acid-Site 67
[UniProt10]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;
Mutagenesis-Variant 112
[Yew04, UniProt11]
Alternate sequence: E → A; UniProt: 0.5% of wild-type activity.
Mutagenesis-Variant 136
[Yew04, UniProt11]
Alternate sequence: H → A; UniProt: 5% of wild-type activity.
Mutagenesis-Variant 139
[Yew04, UniProt11]
Alternate sequence: R → V; UniProt: 17% of wild-type activity.
Amino-Acid-Sites-That-Bind 192
[UniProt10]
UniProt: Substrate;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


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

Campos02: Campos E, Aguilar J, Baldoma L, Badia J (2002). "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli." J Bacteriol 184(21);6065-8. PMID: 12374842

Campos04: Campos E, Baldoma L, Aguilar J, Badia J (2004). "Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in LaAscorbate dissimilation in Escherichia coli." J Bacteriol 186(6);1720-8. PMID: 14996803

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, 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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Wise02: Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I (2002). "Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase." Biochemistry 41(12);3861-9. PMID: 11900527

Wise03: Wise EL, Yew WS, Gerlt JA, Rayment I (2003). "Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily." Biochemistry 42(42);12133-42. PMID: 14567674

Wise04: Wise EL, Yew WS, Gerlt JA, Rayment I (2004). "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase." Biochemistry 43(21);6438-46. PMID: 15157078

Wise05: Wise EL, Yew WS, Akana J, Gerlt JA, Rayment I (2005). "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase." Biochemistry 44(6);1816-23. PMID: 15697207

Yew02: Yew WS, Gerlt JA (2002). "Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons." J Bacteriol 2002;184(1);302-6. PMID: 11741871

Yew04: Yew WS, Wise EL, Rayment I, Gerlt JA (2004). "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase." Biochemistry 43(21);6427-37. PMID: 15157077

Yew05: Yew WS, Akana J, Wise EL, Rayment I, Gerlt JA (2005). "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase." Biochemistry 44(6);1807-15. PMID: 15697206

Other References Related to Gene Regulation

Zhang03c: Zhang Z, Aboulwafa M, Smith MH, Saier MH (2003). "The ascorbate transporter of Escherichia coli." J Bacteriol 185(7);2243-50. PMID: 12644495


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 Tue Nov 25, 2014, biocyc13.