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Escherichia coli K-12 substr. MG1655 Enzyme: oxalyl-CoA decarboxylase



Gene: oxc Accession Numbers: G7236 (EcoCyc), b2373, ECK2369

Synonyms: yfdU

Regulation Summary Diagram: ?

Regulation summary diagram for oxc

Subunit composition of oxalyl-CoA decarboxylase = [Oxc]4
         oxalyl-CoA decarboxylase = Oxc

Summary:
Oxc is the E. coli ortholog of the oxalyl-CoA decarboxylase from Oxalobacter formigenes. The enzyme has oxalyl-CoA decarboxylase activity and may be used for oxalate detoxification [Werther10].

Crystal structures of the apoenzyme and in complex with ADP or the substrate analog acetyl-CoA have been solved. The crystal structure indicates that the enzyme is a tetramer assembled as a dimer of dimers [Werther10].

Oxc is required during the adaption phase of an oxalate-induced acid tolerance response [Fontenot13].

Gene Citations: [Masuda02, Masuda03]

Map Position: [2,488,278 <- 2,489,972] (53.63 centisomes, 193°)
Length: 1695 bp / 564 aa

Molecular Weight of Polypeptide: 60.581 kD (from nucleotide sequence)

Molecular Weight of Multimer: 230.0 kD (experimental) [Werther10]

Unification Links: ASAP:ABE-0007826 , DIP:DIP-48075N , EchoBASE:EB3895 , EcoGene:EG14143 , EcoliWiki:b2373 , Mint:MINT-7717811 , ModBase:P0AFI0 , OU-Microarray:b2373 , PortEco:oxc , Pride:P0AFI0 , Protein Model Portal:P0AFI0 , RefSeq:NP_416874 , RegulonDB:G7236 , SMR:P0AFI0 , String:511145.b2373 , Swiss-Model:P0AFI0 , UniProt:P0AFI0

Relationship Links: InterPro:IN-FAMILY:IPR011766 , InterPro:IN-FAMILY:IPR012000 , InterPro:IN-FAMILY:IPR012001 , InterPro:IN-FAMILY:IPR017660 , InterPro:IN-FAMILY:IPR029035 , InterPro:IN-FAMILY:IPR029061 , PDB:Structure:2Q27 , PDB:Structure:2Q28 , PDB:Structure:2Q29 , Pfam:IN-FAMILY:PF00205 , Pfam:IN-FAMILY:PF02775 , Pfam:IN-FAMILY:PF02776 , Prosite:IN-FAMILY:PS00187

In Paralogous Gene Group: 144 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for oxc

GO Terms:

Biological Process: GO:0033611 - oxalate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01, Werther10]
GO:0071468 - cellular response to acidic pH Inferred from experiment [Fontenot13]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA01, Werther10]
GO:0008949 - oxalyl-CoA decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Werther10]
GO:0030976 - thiamine pyrophosphate binding Inferred from experiment Inferred by computational analysis [GOA01, Werther10]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Werther10]
GO:0043531 - ADP binding Inferred from experiment [Werther10]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]

Gene Class: UNCLASSIFIED

Essentiality data for oxc 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]

Credits:
Created 17-Jun-2010 by Keseler I , SRI International
Last-Curated ? 13-Feb-2013 by Keseler I , SRI International


Enzymatic reaction of: oxalyl-CoA decarboxylase

EC Number: 4.1.1.8

oxalyl-CoA + H+ <=> CO2 + formyl-CoA

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Inhibitors (Competitive): coenzyme A [Werther10]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
oxalyl-CoA
4.8
60.7
12.65
[Werther10, BRENDA14]

pH(opt): 5.5 [BRENDA14, Werther10], 5.5-7 [Werther10]


Sequence Features

Protein sequence of oxalyl-CoA decarboxylase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 32
[UniProt15]
UniProt: Substrate; via amide nitrogen.
Amino-Acid-Sites-That-Bind 118
[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 158
[Werther10, UniProt14]
UniProt: ADP.
Amino-Acid-Sites-That-Bind 220
[Werther10, UniProt14]
UniProt: ADP.
Protein-Segment 261 -> 265
[UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 280
[Werther10, UniProt14]
UniProt: ADP.
Amino-Acid-Sites-That-Bind 302
[Werther10, UniProt14]
UniProt: ADP.
Amino-Acid-Sites-That-Bind 322
[Werther10, UniProt14]
UniProt: ADP; via amide nitrogen.
Amino-Acid-Sites-That-Bind 355
[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 372
[Werther10, UniProt14]
UniProt: Thiamine pyrophosphate.
Protein-Segment 396 -> 398
[UniProt14]
UniProt: Thiamine pyrophosphate binding; Sequence Annotation Type: region of interest.
Protein-Segment 403 -> 404
[UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Protein-Segment 421 -> 423
[UniProt14]
UniProt: Thiamine pyrophosphate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 447
[Werther10, UniProt14]
UniProt: Magnesium.
Protein-Segment 448 -> 449
[UniProt14]
UniProt: Thiamine pyrophosphate binding; Sequence Annotation Type: region of interest.
Metal-Binding-Site 474
[Werther10, UniProt14]
UniProt: Magnesium.
Metal-Binding-Site 476
[Werther10, UniProt14]
UniProt: Magnesium; via carbonyl oxygen.
Amino-Acid-Sites-That-Bind 478
[Werther10, UniProt14]
UniProt: Thiamine pyrophosphate; via amide nitrogen.
Protein-Segment 550 -> 552
[UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

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

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

Fontenot13: Fontenot EM, Ezelle KE, Gabreski LN, Giglio ER, McAfee JM, Mills AC, Qureshi MN, Salmon KM, Toyota CG (2013). "YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12." J Bacteriol 195(7);1446-55. PMID: 23335415

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.

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

Masuda02: Masuda N, Church GM (2002). "Escherichia coli gene expression responsive to levels of the response regulator EvgA." J Bacteriol 184(22);6225-34. PMID: 12399493

Masuda03: Masuda N, Church GM (2003). "Regulatory network of acid resistance genes in Escherichia coli." Mol Microbiol 48(3);699-712. PMID: 12694615

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

Werther10: Werther T, Zimmer A, Wille G, Golbik R, Weiss MS, Konig S (2010). "New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli." FEBS J 277(12);2628-40. PMID: 20553497

Other References Related to Gene Regulation

Itou09: Itou J, Eguchi Y, Utsumi R (2009). "Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12." Biosci Biotechnol Biochem 73(4);870-8. PMID: 19352034


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 19.0 on Sat Aug 1, 2015, biocyc13.