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Escherichia coli K-12 substr. MG1655 Enzyme: UDP-L-Ara4N formyltransferase / UDP-GlcA C-4"-decarboxylase



Gene: arnA Accession Numbers: G7168 (EcoCyc), b2255, ECK2248

Synonyms: SAF, yfbG, pmrI

Regulation Summary Diagram: ?

Subunit composition of UDP-L-Ara4N formyltransferase / UDP-GlcA C-4"-decarboxylase = [ArnA]6
         fused UDP-L-Ara4N formyltransferase and UDP-GlcA C-4''-decarboxylase = ArnA

Summary:
ArnA is a bifunctional enzyme that acts within a pathway that modifies lipid A phosphates with 4-amino-4-deoxy-L-arabinose (L-Ara4N), which causes increased resistance to polymyxin [Breazeale02].

ArnA exhibits UDP-glucuronic acid (UDP-GlcA) C-4"-dehydrogenase and UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) formyltransferase activities in vitro [Breazeale02]. The two activities are separable, but both are required for polymyxin resistance [Breazeale05]. The C-terminal domain contains the NAD+-dependent dehydrogenase/decarboxylase activity. Crystal structures of this domain has been solved at 2.4 and 2.3 Å resolution [GatzevaTopalova04, Williams05a], and active site residues have been identified [Williams05a, GatzevaTopalova05]. The amino terminal domain is similar to methionyl-tRNAfMet formyltransferase and catalyzes the N-10-formyltetrahydrofolate-dependent formylation of the 4'' amine of UDP-L-Ara4N [Breazeale05]. Crystal structures of this domain has been solved at 1.7 and 1.2 Å resolution [GatzevaTopalova05a, Williams05a]. The N-10-formyltetrahydrofolate binding site has been identified and a reaction mechanism has been proposed; point mutations in the proposed catalytic residues abolish activity [GatzevaTopalova05a, Williams05a]. Crystal structures of the full-length protein and various point mutants have been solved [GatzevaTopalova05].

ArnA was also identified as a protein that copurifies with the SsrA-SmpB complex [Karzai01].

SAF: "SsrA-associated factor" [Karzai01]

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

PmrI: "polymyxin resistance"

Review: [Raetz07]

Locations: cytosol

Map Position: [2,366,061 -> 2,368,043] (51.0 centisomes)
Length: 1983 bp / 660 aa

Molecular Weight of Polypeptide: 74.289 kD (from nucleotide sequence), 73.0 kD (experimental) [Breazeale02 ]

Unification Links: ASAP:ABE-0007460 , DIP:DIP-11961N , EchoBASE:EB3844 , EcoGene:EG14091 , EcoliWiki:b2255 , Mint:MINT-1257581 , ModBase:P77398 , OU-Microarray:b2255 , PortEco:arnA , PR:PRO_000022138 , Pride:P77398 , Protein Model Portal:P77398 , RefSeq:NP_416758 , RegulonDB:G7168 , SMR:P77398 , String:511145.b2255 , UniProt:P77398

Relationship Links: InterPro:IN-FAMILY:IPR001509 , InterPro:IN-FAMILY:IPR002376 , InterPro:IN-FAMILY:IPR005793 , InterPro:IN-FAMILY:IPR011034 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR021168 , PDB:Structure:1U9J , PDB:Structure:1YRW , PDB:Structure:1Z73 , PDB:Structure:1Z74 , PDB:Structure:1Z75 , PDB:Structure:1Z7B , PDB:Structure:1Z7E , PDB:Structure:2BLL , PDB:Structure:2BLN , Pfam:IN-FAMILY:PF00551 , Pfam:IN-FAMILY:PF01370 , Pfam:IN-FAMILY:PF02911

In Paralogous Gene Group: 397 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009245 - lipid A biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GatzevaTopalova05a]
GO:0033320 - UDP-D-xylose biosynthetic process Inferred from experiment [Polizzi12]
GO:0046677 - response to antibiotic Inferred from experiment Inferred by computational analysis [UniProtGOA11, Breazeale05]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11]
GO:0046493 - lipid A metabolic process Inferred by computational analysis [GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred from experiment Inferred by computational analysis [GOA06, GatzevaTopalova04]
GO:0016742 - hydroxymethyl-, formyl- and related transferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GatzevaTopalova05a]
GO:0048040 - UDP-glucuronate decarboxylase activity Inferred from experiment [Polizzi12]
GO:0070403 - NAD+ binding Inferred from experiment [Polizzi12]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0050662 - coenzyme binding Inferred by computational analysis [GOA01]
Cellular Component: 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 arnA 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:
Created 22-Jul-2008 by Keseler I , SRI International
Last-Curated ? 22-Jul-2008 by Keseler I , SRI International


Enzymatic reaction of: UDP-L-Ara4N formyltransferase

EC Number: 2.1.2.13

UDP-4-amino-4-deoxy-β-L-arabinopyranose + an N10-formyl-tetrahydrofolate <=> UDP-4-deoxy-4-formamido-β-L-arabinopyranose + a tetrahydrofolate + H+

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 physiologically favored in the direction shown.

In Pathways: polymyxin resistance


Enzymatic reaction of: UDP-GlcA C-4"-decarboxylase

Synonyms: UDP-glucuronic acid C-4"-decarboxylase

EC Number: 1.1.1.305

UDP-α-D-glucuronate + NAD+ <=> UDP-β-L-threo-pentapyranos-4-ulose + CO2 + NADH

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 physiologically favored in the direction shown.

In Pathways: polymyxin resistance

Kinetic Parameters:

Substrate
Km (μM)
Citations
UDP-α-D-glucuronate
86.0
[GatzevaTopalova04]
NAD+
760.0
[GatzevaTopalova04]


Sequence Features

Feature Class Location Common Name Catalytic Activity Citations Comment
Protein-Segment 1 -> 304    
[UniProt10]
UniProt: Formyltransferase ArnAFT; Sequence Annotation Type: region of interest;
Catalytic-Domain 1 -> 313 formyltransferase domain UDP-L-Ara4N formyltransferase
[Breazeale05, GatzevaTopalova05a]
 
Protein-Segment 86 -> 88    
[UniProt10]
UniProt: 10-formyltetrahydrofolate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 102    
[GatzevaTopalova05a, UniProt11a]
Alternate sequence: N → A; UniProt: No activity.
Amino-Acid-Site 102    
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;
Mutagenesis-Variant 104    
[GatzevaTopalova05a, UniProt11a]
Alternate sequence: H → K; UniProt: Less than 1% residual activity.
Alternate sequence: H → A; UniProt: 25-fold lower activity.
Active-Site 104    
[UniProt10a]
UniProt: Proton donor; for formyltransferase activity;
Amino-Acid-Sites-That-Bind 114    
[UniProt10a]
UniProt: 10-formyltetrahydrofolate;
Protein-Segment 136 -> 140    
[UniProt10]
UniProt: 10-formyltetrahydrofolate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 140    
[GatzevaTopalova05a, UniProt11a]
Alternate sequence: D → N; UniProt: Less than 1% residual activity.
Alternate sequence: D → A; UniProt: Less than 1% residual activity.
Amino-Acid-Site 140    
[UniProt10a]
UniProt: Raises pKa of active site His; Sequence Annotation Type: site;
Catalytic-Domain 314 -> 660 decarboxylase domain UDP-GlcA C-4"-decarboxylase
[GatzevaTopalova04]
 
Amino-Acid-Sites-That-Bind 347    
[UniProt10a]
UniProt: NAD;
Nucleotide-Phosphate-Binding-Region 368 -> 369    
[UniProt10a]
UniProt: NAD binding;
Amino-Acid-Sites-That-Bind 393    
[UniProt10a]
UniProt: UDP-glucuronate; via carbonyl oxygen;
Amino-Acid-Sites-That-Bind 398    
[UniProt10a]
UniProt: UDP-glucuronate;
Protein-Segment 432 -> 433    
[UniProt10]
UniProt: UDP-glucuronate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 433    
[GatzevaTopalova05, Williams05a, UniProt11a]
Alternate sequence: S → T; UniProt: No activity.
Alternate sequence: S → A; UniProt: 40-fold lower specific activity.
Mutagenesis-Variant 434    
[Williams05a, UniProt11a]
Alternate sequence: E → Q; UniProt: No activity.
Alternate sequence: E → A; UniProt: 100-fold lower specific activity.
Active-Site 434    
[UniProt10a]
UniProt: Proton acceptor; for decarboxylase activity;
Amino-Acid-Sites-That-Bind 460    
[UniProt10a]
UniProt: UDP-glucuronate;
Amino-Acid-Sites-That-Bind 492    
[UniProt10a]
UniProt: UDP-glucuronate;
Protein-Segment 526 -> 535    
[UniProt10]
UniProt: UDP-glucuronate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 613    
[UniProt10a]
UniProt: UDP-glucuronate;
Mutagenesis-Variant 619    
[GatzevaTopalova05, UniProt11a]
Alternate sequence: R → M; UniProt: 400-fold lower activity.
Alternate sequence: R → Y; UniProt: No activity.
Alternate sequence: R → E; UniProt: No activity.
Active-Site 619    
[UniProt10a]
UniProt: Proton donor; for decarboxylase activity;


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

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

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

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

GatzevaTopalova04: Gatzeva-Topalova PZ, May AP, Sousa MC (2004). "Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance." Biochemistry 43(42);13370-9. PMID: 15491143

GatzevaTopalova05: Gatzeva-Topalova PZ, May AP, Sousa MC (2005). "Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance." Structure (Camb) 13(6);929-42. PMID: 15939024

GatzevaTopalova05a: Gatzeva-Topalova PZ, May AP, Sousa MC (2005). "Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance." Biochemistry 44(14);5328-38. PMID: 15807526

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

Karzai01: Karzai AW, Sauer RT (2001). "Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex." Proc Natl Acad Sci U S A 98(6);3040-4. PMID: 11248028

Polizzi12: Polizzi SJ, Walsh RM, Peeples WB, Lim JM, Wells L, Wood ZA (2012). "Human UDP-α-D-xylose synthase and Escherichia coli ArnA conserve a conformational shunt that controls whether xylose or 4-keto-xylose is produced." Biochemistry 51(44);8844-55. PMID: 23072385

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: 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.

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."

Williams05a: Williams GJ, Breazeale SD, Raetz CR, Naismith JH (2005). "Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis." J Biol Chem 280(24);23000-8. PMID: 15809294

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

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

Lee05b: 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 Fri Nov 28, 2014, biocyc13.