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Escherichia coli K-12 substr. MG1655 Enzyme: γ-butyrobetainyl-CoA:carnitine CoA transferase



Gene: caiB Accession Numbers: EG11559 (EcoCyc), b0038, ECK0039

Synonyms: yaaN

Regulation Summary Diagram: ?

Subunit composition of γ-butyrobetainyl-CoA:carnitine CoA transferase = [CaiB]2
         CaiB monomer = CaiB

Summary:
The crystal structure of CaiB has been solved and shows that two monomers form an interlaced dimer [Stenmark04].

CaiB was thought to be a carnitine dehydratase ([Jung89, Eichler94a]), but was later shown to be a type III CoA transferase [Elssner01]. The purified CaiB likely contained small amounts of CaiD, accounting for the observed activity [Elssner01].

In E. coli strain O44 K74, the caiB gene product forms a complex with the caiA gene product, crotonobetaine reductase. [Preusser99]

Gene Citations: [Eichler94, Eichler96]

Locations: cytosol

Map Position: [37,898 <- 39,115] (0.82 centisomes)
Length: 1218 bp / 405 aa

Molecular Weight of Polypeptide: 45.127 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000136 , CGSC:36800 , EchoBASE:EB1520 , EcoGene:EG11559 , EcoliWiki:b0038 , ModBase:P31572 , OU-Microarray:b0038 , PortEco:caiB , PR:PRO_000022242 , Pride:P31572 , Protein Model Portal:P31572 , RefSeq:NP_414580 , RegulonDB:EG11559 , SMR:P31572 , String:511145.b0038 , UniProt:P31572

Relationship Links: InterPro:IN-FAMILY:IPR003673 , InterPro:IN-FAMILY:IPR023452 , InterPro:IN-FAMILY:IPR023606 , Panther:IN-FAMILY:PTHR11837 , PDB:Structure:1XA3 , PDB:Structure:1XA4 , PDB:Structure:1XK6 , PDB:Structure:1XK7 , PDB:Structure:1XVT , PDB:Structure:1XVU , PDB:Structure:1XVV , Pfam:IN-FAMILY:PF02515

In Paralogous Gene Group: 14 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0042413 - carnitine catabolic process Inferred from experiment [Eichler94a]
GO:0009437 - carnitine metabolic process Inferred by computational analysis [UniProtGOA12, GOA01]
Molecular Function: GO:0008735 - carnitine dehydratase activity Inferred from experiment [Eichler94a, Eichler94]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008410 - CoA-transferase activity Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016782 - transferase activity, transferring sulfur-containing groups Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism carnitine metabolism

Essentiality data for caiB 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]

Enzymatic reaction of: γ-butyrobetainyl-CoA:carnitine CoA transferase

EC Number: 2.8.3.21

L-carnitine + γ-butyrobetainyl-CoA <=> L-carnitinyl-CoA + γ-butyrobetaine

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

The reaction is favored in the direction shown.

In Pathways: L-carnitine degradation I


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 97
[UniProt10]
UniProt: Coenzyme A;
Amino-Acid-Sites-That-Bind 104
[UniProt10]
UniProt: Coenzyme A;
Active-Site 169
[UniProt10]
UniProt: Nucleophile;
Extrinsic-Sequence-Variant 187
[UniProt10]
Alternate sequence: V → A; UniProt: (in strain: O44:K74);
Extrinsic-Sequence-Variant 302
[UniProt10]
Alternate sequence: T → A; UniProt: (in strain: O44:K74);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0038 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11559; 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

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

Eichler94: Eichler K, Bourgis F, Buchet A, Kleber HP, Mandrand-Berthelot MA (1994). "Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli." Mol Microbiol 1994;13(5);775-86. PMID: 7815937

Eichler94a: Eichler K, Schunck WH, Kleber HP, Mandrand-Berthelot MA (1994). "Cloning, nucleotide sequence, and expression of the Escherichia coli gene encoding carnitine dehydratase." J Bacteriol 1994;176(10);2970-5. PMID: 8188598

Eichler96: Eichler K, Buchet A, Lemke R, Kleber HP, Mandrand-Berthelot MA (1996). "Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli." J Bacteriol 1996;178(5);1248-57. PMID: 8631699

Elssner01: Elssner T, Engemann C, Baumgart K, Kleber HP (2001). "Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli." Biochemistry 40(37);11140-8. PMID: 11551212

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."

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

Jung89: Jung H, Jung K, Kleber HP (1989). "Purification and properties of carnitine dehydratase from Escherichia coli--a new enzyme of carnitine metabolization." Biochim Biophys Acta 1989;1003(3);270-6. PMID: 2663076

Preusser99: Preusser A, Wagner U, Elssner T, Kleber HP (1999). "Crotonobetaine reductase from Escherichia coli consists of two proteins." Biochim Biophys Acta 1999;1431(1);166-78. PMID: 10209289

Stenmark04: Stenmark P, Gurmu D, Nordlund P (2004). "Crystal structure of CaiB, a type-III CoA transferase in carnitine metabolism." Biochemistry 43(44);13996-4003. PMID: 15518548

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

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

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

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

Other References Related to Gene Regulation

Beisel12: Beisel CL, Updegrove TB, Janson BJ, Storz G (2012). "Multiple factors dictate target selection by Hfq-binding small RNAs." EMBO J 31(8);1961-74. PMID: 22388518

Buchet98: Buchet A, Eichler K, Mandrand-Berthelot MA (1998). "Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region." J Bacteriol 1998;180(10);2599-608. PMID: 9573142

Buchet99: Buchet A, Nasser W, Eichler K, Mandrand-Berthelot MA (1999). "Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator." Mol Microbiol 1999;34(3);562-75. PMID: 10564497

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Liu04: Liu X, De Wulf P (2004). "Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling." J Biol Chem 279(13);12588-97. PMID: 14711822

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220


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 Sat Nov 22, 2014, BIOCYC14A.