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Escherichia coli K-12 substr. MG1655 Enzyme: UDP-L-Ara4O C-4" transaminase



Gene: arnB Accession Numbers: G7166 (EcoCyc), b2253, ECK2246

Synonyms: pmrH, yfbE

Regulation Summary Diagram: ?

Summary:
ArnB is a UDP-L-Ara4O C-4" transaminase [Breazeale03] that acts in a pathway which modifies lipid A phosphates with 4-amino-4-deoxy-L-arabinose (L-Ara4N), causing increased resistance to polymyxin [Breazeale02].

Structural and biochemical characterization of Salmonella typhimurium ArnB has been performed; crystal structures of the enzyme are presented and discussed with respect to catalysis [Noland02].

Expression of arnB is induced by the presence of FeSO4 (which primarily yields oxidized ferric iron in solution); the effect is dependent on the presence of the BasS-BasR two-component system [Hagiwara04, Froelich06].

ArnB: "L-Ara4N (4-amino-4-deoxy-L-arabinose) biosynthesis" [Breazeale02]

PmrH: "polymyxin resistance"

Review: [Raetz07]

Locations: cytosol

Map Position: [2,363,932 -> 2,365,089] (50.95 centisomes)
Length: 1158 bp / 385 aa

Molecular Weight of Polypeptide: 42.238 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007456 , EchoBASE:EB3842 , EcoGene:EG14089 , EcoliWiki:b2253 , ModBase:P77690 , OU-Microarray:b2253 , PortEco:arnB , PR:PRO_000022139 , Pride:P77690 , Protein Model Portal:P77690 , RefSeq:NP_416756 , RegulonDB:G7166 , SMR:P77690 , String:511145.b2253 , Swiss-Model:P77690 , UniProt:P77690

Relationship Links: InterPro:IN-FAMILY:IPR000653 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR022850 , Pfam:IN-FAMILY:PF01041

In Paralogous Gene Group: 395 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
GO:0009245 - lipid A biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0046493 - lipid A metabolic process Inferred by computational analysis [GOA06]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008483 - transaminase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Breazeale03]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01a, Breazeale03]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Author statement [Breazeale03]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection drug resistance/sensitivity
metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide lipid A

Essentiality data for arnB knockouts: ?

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

Credits:
Last-Curated ? 21-Jul-2008 by Keseler I , SRI International


Enzymatic reaction of: UDP-L-Ara4O C-4" transaminase

EC Number: 2.6.1.87

UDP-4-amino-4-deoxy-β-L-arabinopyranose + 2-oxoglutarate <=> UDP-β-L-threo-pentapyranos-4-ulose + L-glutamate

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. [Breazeale03]

Alternative Substrates for L-glutamate: L-2-aminoadipate [Breazeale03 ]

In Pathways: polymyxin resistance

Summary:
ArnB activity can be assayed in both directions; the equilibrium constant in the direction of UDP-L-Ara4N formation is ~0.1, i.e. favoring UDP-L-Ara4O formation [Breazeale03].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Breazeale03]


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 182
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine; 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 ].
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

Breazeale02: Breazeale SD, Ribeiro AA, Raetz CR (2002). "Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose." J Biol Chem 277(4);2886-96. PMID: 11706007

Breazeale03: Breazeale SD, Ribeiro AA, Raetz CR (2003). "Origin of lipid A species modified with 4-amino-4-deoxy-L-arabinose in polymyxin-resistant mutants of Escherichia coli. An aminotransferase (ArnB) that generates UDP-4-deoxyl-L-arabinose." J Biol Chem 278(27);24731-9. PMID: 12704196

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

Froelich06: Froelich JM, Tran K, Wall D (2006). "A pmrA constitutive mutant sensitizes Escherichia coli to deoxycholic acid." J Bacteriol 188(3);1180-3. PMID: 16428424

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."

Hagiwara04: Hagiwara D, Yamashino T, Mizuno T (2004). "A Genome-wide view of the Escherichia coli BasS-BasR two-component system implicated in iron-responses." Biosci Biotechnol Biochem 68(8);1758-67. PMID: 15322361

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

Noland02: Noland BW, Newman JM, Hendle J, Badger J, Christopher JA, Tresser J, Buchanan MD, Wright TA, Rutter ME, Sanderson WE, Muller-Dieckmann HJ, Gajiwala KS, Buchanan SG (2002). "Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme." Structure (Camb) 10(11);1569-80. PMID: 12429098

Raetz07: Raetz CR, Reynolds CM, Trent MS, Bishop RE (2007). "Lipid A modification systems in gram-negative bacteria." Annu Rev Biochem 76;295-329. PMID: 17362200

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Other References Related to Gene Regulation

Lee05a: Lee LJ, Barrett JA, Poole RK (2005). "Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc." J Bacteriol 187(3);1124-34. PMID: 15659689

Ogasawara12: Ogasawara H, Shinohara S, Yamamoto K, Ishihama A (2012). "Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli." Microbiology 158(Pt 6);1482-92. PMID: 22442305


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 Wed Nov 26, 2014, BIOCYC14B.