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Escherichia coli K-12 substr. MG1655 Enzyme: D-glucarate dehydratase



Gene: gudD Accession Numbers: G7445 (EcoCyc), b2787, ECK2781

Synonyms: ygcX

Regulation Summary Diagram: ?

Summary:
D-glucarate dehydratase catalyzes the dehydration of D-glucarate to 5-keto-4-deoxy-D-glucarate (KDG).

Crystal structure of the enzyme alone and bound to the product or competitive inhibitors have been solved. The structures allowed the identification of active site residues and ligands for the Mg2+ cofactor. Further kinetic and structural analysis led to a proposed reaction mechanism involving an enediolate anion intermediate. Formation of this intermediate from both D-glucarate and L-idarate is the kinetically reversible first step in the overall reaction, accounting for the apparent D-glucarate/L-idarate epimerase activity of the enzyme [Gulick00, Gulick01].

Enzymatic activity of D-glucarate dehydratase is induced by growth on D-glucarate, D-galactarate, and D-glycerate [Monterrubio00].

Review: [Gerlt05]

Citations: [Roberton80]

Locations: cytosol

Map Position: [2,916,067 <- 2,917,407] (62.85 centisomes)
Length: 1341 bp / 446 aa

Molecular Weight of Polypeptide: 49.141 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009134 , EchoBASE:EB2959 , EcoGene:EG13167 , EcoliWiki:b2787 , ModBase:P0AES2 , OU-Microarray:b2787 , PortEco:gudD , PR:PRO_000022853 , Pride:P0AES2 , Protein Model Portal:P0AES2 , RefSeq:NP_417267 , RegulonDB:G7445 , SMR:P0AES2 , String:511145.b2787 , Swiss-Model:P0AES2 , UniProt:P0AES2

Relationship Links: InterPro:IN-FAMILY:IPR001354 , InterPro:IN-FAMILY:IPR013342 , InterPro:IN-FAMILY:IPR017653 , Panther:IN-FAMILY:PTHR13794 , PDB:Structure:1EC7 , PDB:Structure:1EC8 , PDB:Structure:1EC9 , PDB:Structure:1ECQ , PDB:Structure:1JCT , PDB:Structure:1JDF , PDB:Structure:3PWG , PDB:Structure:3PWI , PDB:Structure:4GYP , Pfam:IN-FAMILY:PF01188 , Smart:IN-FAMILY:SM00922

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0042838 - D-glucarate catabolic process Inferred by computational analysis Inferred from experiment [Gulick01, UniProtGOA12, Hubbard98]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0019394 - glucarate catabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0000287 - magnesium ion binding Inferred by computational analysis Inferred from experiment [Gulick01, GOA01]
GO:0008872 - glucarate dehydratase activity Inferred by computational analysis Inferred from experiment [Gulick01, GOA01a, GOA01, Hubbard98]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for gudD 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:
Last-Curated ? 20-Aug-2007 by Keseler I , SRI International


Enzymatic reaction of: L-idarate epimerase (D-glucarate dehydratase)

EC Number: 5.1.2.-

L-idarate <=> D-glucarate

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.

Note: The enzyme may catalyze this reaction in vitro, but this reaction is not considered to be physiologically relevant.

Summary:
L-idarate is an unnatural diacid sugar and the GudD catalysed epimerisation reaction is not considered physiologically relevant. The promiscuity of the GudP enzyme is assumed to be 'an in vitro accident' [Gerlt05].|

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-glucarate
60.0
[Hubbard98]
L-idarate
16.0
[Hubbard98]


Enzymatic reaction of: D-glucarate dehydratase

Synonyms: D-glucarate dehydrase, D-glucarate hydro-lyase, GDH, GlucD

EC Number: 4.2.1.40

D-glucarate <=> 5-dehydro-4-deoxy-D-glucarate + H2O

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 irreversible in the direction shown.

Alternative Substrates for D-glucarate: L-idarate [Hubbard98 ]

In Pathways: superpathway of D-glucarate and D-galactarate degradation , D-glucarate degradation I

Summary:
The enzyme was originally isolated from E. coli strain CR63MA, but is present in other strains including K-12 [BLUMENTHAL63, Blumenthal66]

The Km for L-idarate is 16 µM [Hubbard98].

Cofactors or Prosthetic Groups: Mg2+ [Comment 5, Gulick00]

Inhibitors (Competitive): xylarohydroxamate [Gulick00] , 4-deoxy-D-glucarate [Gulick00]

Inhibitors (Unknown Mechanism): D-idarate [Blumenthal66] , Mn2+ [Comment 6] , Co2+ [Comment 7] , p-chloromercuriphenylsulfonate [Blumenthal66] , D-galactarate [Blumenthal66] , L-tartrate [Blumenthal66]

Primary Physiological Regulators of Enzyme Activity: D-galactarate , L-tartrate

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-glucarate
60.0
[Hubbard98]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Hubbard98]
 
Chain 2 -> 446
[UniProt09]
UniProt: Glucarate dehydratase;
Amino-Acid-Sites-That-Bind 32
[UniProt12]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 103
[UniProt12]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 150
[UniProt12]
UniProt: Substrate.
Mutagenesis-Variant 150
[Gulick00, UniProt11a]
Alternate sequence: Y → F; UniProt: Reduces activity 100-fold.
Amino-Acid-Sites-That-Bind 205
[UniProt12]
UniProt: Substrate.
Mutagenesis-Variant 207
[Gulick00, UniProt11a]
Alternate sequence: K → R; UniProt: Reduces activity 10000-fold.
Alternate sequence: K → Q; UniProt: Reduces activity 1000-fold.
Active-Site 207
[UniProt10]
UniProt: Proton acceptor;
Protein-Segment 235 -> 237
[UniProt12]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 235
[UniProt10]
UniProt: Magnesium;
Metal-Binding-Site 266
[UniProt10]
UniProt: Magnesium;
Metal-Binding-Site 289
[UniProt10]
UniProt: Magnesium;
Sequence-Conflict 310 -> 313
[Blattner97, UniProt10]
Alternate sequence: PLAD → RWRI; UniProt: (in Ref. 1; AAB40437);
Protein-Segment 339 -> 341
[UniProt12]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 339
[Gulick00, UniProt11a]
Alternate sequence: H → Q; UniProt: Reduces activity 1000-fold.
Alternate sequence: H → N; UniProt: Reduces activity 10000-fold.
Alternate sequence: H → A; UniProt: Loss of activity.
Active-Site 339
[UniProt10]
UniProt: Proton acceptor;
Mutagenesis-Variant 366
[Gulick00, UniProt11a]
Alternate sequence: D → N; UniProt: Reduces activity over 100-fold.
Alternate sequence: D → A; UniProt: Reduces activity over 100-fold.
Amino-Acid-Sites-That-Bind 368
[UniProt12]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 422
[UniProt12]
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

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

BLUMENTHAL63: Blumenthal HJ, Fish DC (1963). "Bacterial conversion of D-glucarate to glycerate and pyruvate." Biochem Biophys Res Comm1963;11(3):239-243. PMID: 13971911

Blumenthal66: Blumenthal H "D-Glucarate Dehydrase." Meth Enz 1966;9:660-665.

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

Gerlt05: Gerlt JA, Babbitt PC, Rayment I (2005). "Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity." Arch Biochem Biophys 433(1);59-70. PMID: 15581566

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.

Gulick00: Gulick AM, Hubbard BK, Gerlt JA, Rayment I (2000). "Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli." Biochemistry 2000;39(16);4590-602. PMID: 10769114

Gulick01: Gulick AM, Hubbard BK, Gerlt JA, Rayment I (2001). "Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli." Biochemistry 40(34);10054-62. PMID: 11513584

Hubbard98: Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA (1998). "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli." Biochemistry 1998;37(41);14369-75. PMID: 9772162

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

Monterrubio00: Monterrubio R, Baldoma L, Obradors N, Aguilar J, Badia J (2000). "A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli." J Bacteriol 2000;182(9);2672-4. PMID: 10762278

Roberton80: Roberton AM, Sullivan PA, Jones-Mortimer MC, Kornberg HL (1980). "Two genes affecting glucarate utilization in Escherichia coli K12." J Gen Microbiol 1980;117(2);377-82. PMID: 6999115

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProtGOA11: 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."

Other References Related to Gene Regulation

Sampaio04: Sampaio MM, Chevance F, Dippel R, Eppler T, Schlegel A, Boos W, Lu YJ, Rock CO (2004). "Phosphotransferase-mediated transport of the osmolyte 2-O-alpha-mannosyl-D-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor." J Biol Chem 279(7);5537-48. PMID: 14645248


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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 18.5 on Sun Dec 21, 2014, BIOCYC13A.