Escherichia coli K-12 substr. MG1655 Polypeptide: conserved protein

Gene: arnD Accession Numbers: G7169 (EcoCyc), b2256, ECK2249

Synonyms: pmrJ, yfbH

Regulation Summary Diagram: ?

Regulation summary diagram for arnD

ArnD is predicted to act as a deformylase that removes the formyl group from undecaprenyl phosphate-L-Ara4FN [Breazeale05, Yan07].

Deletion of arnD results in restoration of polymyxin sensitivity in a polymyxin-resitant pmrAc strain [Yan07].

Expression of the arnBCADTEF operon increased during growth with elevated FeSO4, FeCl3, or ZnSO4 and was dependent upon the BasSR two-component signal transduction system [Hagiwara04, Lee05d].

Citations: [Zhou99a, Nummila95, Groisman01, Trent01, Gibbons05]

Locations: cytosol

Map Position: [2,368,040 -> 2,368,930] (51.04 centisomes, 184°)
Length: 891 bp / 296 aa

Molecular Weight of Polypeptide: 33.112 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007462 , EchoBASE:EB3845 , EcoGene:EG14092 , EcoliWiki:b2256 , ModBase:P76472 , OU-Microarray:b2256 , PortEco:arnD , Pride:P76472 , Protein Model Portal:P76472 , RefSeq:NP_416759 , RegulonDB:G7169 , String:511145.b2256 , UniProt:P76472

Relationship Links: InterPro:IN-FAMILY:IPR002509 , InterPro:IN-FAMILY:IPR011330 , InterPro:IN-FAMILY:IPR023557 , Pfam:IN-FAMILY:PF01522 , Prosite:IN-FAMILY:PS51677

Genetic Regulation Schematic: ?

Genetic regulation schematic for arnD

GO Terms:

Biological Process: GO:0010041 - response to iron(III) ion Inferred from experiment [Chamnongpol02, Hagiwara04]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
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, GOA06]
GO:0036108 - 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01a]
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides Inferred by computational analysis [GOA06, GOA01, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: ORFs Conserved-Hypothetical-ORFs

Essentiality data for arnD 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]

Curated 22-Jul-2008 by Keseler I , SRI International
Last-Curated ? 01-Aug-2008 by Johnson A , JCVI

Sequence Features

Protein sequence of conserved protein with features indicated

Feature Class Location Citations Comment
Conserved-Region 2 -> 260
UniProt: NodB homology.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Breazeale05: Breazeale SD, Ribeiro AA, McClerren AL, Raetz CR (2005). "A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose." J Biol Chem 280(14);14154-67. PMID: 15695810

Chamnongpol02: Chamnongpol S, Dodson W, Cromie MJ, Harris ZL, Groisman EA (2002). "Fe(III)-mediated cellular toxicity." Mol Microbiol 45(3);711-9. PMID: 12139617

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

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

Gibbons05: Gibbons HS, Kalb SR, Cotter RJ, Raetz CR (2005). "Role of Mg2+ and pH in the modification of Salmonella lipid A after endocytosis by macrophage tumour cells." Mol Microbiol 55(2);425-40. PMID: 15659161

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."

Groisman01: Groisman EA (2001). "The pleiotropic two-component regulatory system PhoP-PhoQ." J Bacteriol 183(6);1835-42. PMID: 11222580

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

Lee05d: 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

Nummila95: Nummila K, Kilpelainen I, Zahringer U, Vaara M, Helander IM (1995). "Lipopolysaccharides of polymyxin B-resistant mutants of Escherichia coli are extensively substituted by 2-aminoethyl pyrophosphate and contain aminoarabinose in lipid A." Mol Microbiol 16(2);271-8. PMID: 7565089

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Trent01: Trent MS, Ribeiro AA, Doerrler WT, Lin S, Cotter RJ, Raetz CR (2001). "Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm." J Biol Chem 276(46);43132-44. PMID: 11535605

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 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."

Yan07: Yan A, Guan Z, Raetz CR (2007). "An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli." J Biol Chem 282(49);36077-89. PMID: 17928292

Zhou99a: Zhou Z, Lin S, Cotter RJ, Raetz CR (1999). "Lipid A modifications characteristic of Salmonella typhimurium are induced by NH4VO3 in Escherichia coli K12. Detection of 4-amino-4-deoxy-L-arabinose, phosphoethanolamine and palmitate." J Biol Chem 274(26);18503-14. PMID: 10373459

Other References Related to Gene Regulation

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

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

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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 19.0 on Fri Oct 9, 2015, biocyc13.