P77398 (ARNA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional polymyxin resistance protein ArnA

Alternative name(s):
Polymyxin resistance protein PmrI

Including the following 2 domains:

1. UDP-4-amino-4-deoxy-L-arabinose formyltransferase
   EC=2.1.2.13
   Alternative name(s):
   ArnAFT
   UDP-L-Ara4N formyltransferase
2. UDP-glucuronic acid oxidase, UDP-4-keto-hexauronic acid decarboxylating
   EC=1.1.1.305
   Alternative name(s):
   ArnADH
   UDP-GlcUA decarboxylase
   UDP-glucuronic acid dehydrogenase

Gene names

Name:	arnA
Synonyms:	pmrI, yfbG
Ordered Locus Names:	b2255, JW2249

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	660 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Bifunctional enzyme that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O) and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. Ref.1 Ref.6
Catalytic activity	UDP-alpha-D-glucuronate + NAD+ = UDP-beta-L-threo-pentapyranos-4-ulose + CO2 + NADH. Ref.6 Ref.8 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose. Ref.6 Ref.8
Pathway	Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 1/3. Ref.7 Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 3/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Ref.7
Subunit structure	Homohexamer, formed by a dimer of trimers. Ref.11
Induction	Induced by BasR. Ref.5
Sequence similarities	In the N-terminal section; belongs to the fmt family. UDP-L-Ara4N formyltransferase subfamily. In the C-terminal section; belongs to the sugar epimerase family. UDP-glucuronic acid decarboxylase subfamily.
Biophysicochemical properties	Kinetic parameters: KM=0.76 mM for NAD Ref.8 KM=0.086 mM for UDP-GlcUA

Ontologies

Keywords
Biological process	Antibiotic resistance Lipid A biosynthesis Lipid biosynthesis Lipid metabolism Lipopolysaccharide biosynthesis
Ligand	NAD
Molecular function	Methyltransferase Oxidoreductase Transferase
Technical term	3D-structure Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	lipid A biosynthetic process Inferred from direct assay Ref.9. Source: EcoCyc lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway response to antibiotic Inferred from direct assay Ref.6. Source: EcoCyc
Molecular_function	coenzyme binding Inferred from electronic annotation. Source: InterPro hydroxymethyl-, formyl- and related transferase activity Inferred from direct assay Ref.9. Source: EcoCyc methyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred from direct assay Ref.8. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ynbC	P76092	1	EBI-545305,EBI-544837

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 660

660

Bifunctional polymyxin resistance protein ArnA HAMAP-Rule MF_01166

PRO_0000083098

Regions

Nucleotide binding

368 – 369

2

NAD binding HAMAP-Rule MF_01166

Region

1 – 304

304

Formyltransferase ArnAFT HAMAP-Rule MF_01166

Region

86 – 88

3

10-formyltetrahydrofolate binding HAMAP-Rule MF_01166

Region

136 – 140

5

10-formyltetrahydrofolate binding HAMAP-Rule MF_01166

Region

314 – 660

347

Dehydrogenase ArnADH HAMAP-Rule MF_01166

Region

432 – 433

2

UDP-glucuronate binding HAMAP-Rule MF_01166

Region

526 – 535

10

UDP-glucuronate binding HAMAP-Rule MF_01166

Sites

Active site

104

1

Proton donor; for formyltransferase activity

Active site

434

1

Proton acceptor; for decarboxylase activity

Active site

619

1

Proton donor; for decarboxylase activity

Binding site

114

1

10-formyltetrahydrofolate

Binding site

347

1

NAD

Binding site

393

1

UDP-glucuronate; via carbonyl oxygen

Binding site

398

1

UDP-glucuronate

Binding site

460

1

UDP-glucuronate

Binding site

492

1

UDP-glucuronate

Binding site

613

1

UDP-glucuronate

Site

102

1

Transition state stabilizer

Site

140

1

Raises pKa of active site His

Experimental info

Mutagenesis

102

1

N → A: No activity. Ref.9

Mutagenesis

104

1

H → A: 25-fold lower activity. Ref.9

Mutagenesis

104

1

H → K: Less than 1% residual activity. Ref.9

Mutagenesis

140

1

D → A or N: Less than 1% residual activity. Ref.9

Mutagenesis

433

1

S → A: 40-fold lower specific activity. Ref.10 Ref.11

Mutagenesis

433

1

S → T: No activity. Ref.10 Ref.11

Mutagenesis

434

1

E → A: 100-fold lower specific activity. Ref.10

Mutagenesis

434

1

E → Q: No activity. Ref.10

Mutagenesis

619

1

R → E or Y: No activity. Ref.11

Mutagenesis

619

1

R → M: 400-fold lower activity. Ref.11

Secondary structure

1

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660

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Helix

9 – 21

13

Beta strand

25 – 30

6

Helix

45 – 52

8

Helix

65 – 73

9

Beta strand

77 – 83

7

Helix

90 – 93

4

Beta strand

100 – 106

7

Turn

108 – 111

4

Beta strand

112 – 114

3

Helix

116 – 122

7

Beta strand

126 – 134

9

Turn

139 – 141

3

Beta strand

144 – 151

8

Helix

158 – 181

24

Helix

192 – 194

3

Helix

203 – 206

4

Helix

214 – 223

10

Beta strand

231 – 235

5

Beta strand

238 – 248

11

Beta strand

258 – 261

4

Turn

262 – 264

3

Beta strand

265 – 268

4

Beta strand

270 – 281

12

Helix

289 – 296

8

Beta strand

299 – 301

3

Beta strand

317 – 322

6

Helix

326 – 337

12

Beta strand

342 – 348

7

Helix

351 – 356

6

Beta strand

362 – 366

5

Turn

369 – 371

3

Helix

374 – 382

9

Beta strand

384 – 388

5

Helix

395 – 400

6

Helix

402 – 409

8

Helix

411 – 422

12

Beta strand

426 – 430

5

Helix

433 – 436

4

Beta strand

442 – 444

3

Turn

446 – 448

3

Beta strand

451 – 453

3

Helix

459 – 461

3

Helix

462 – 481

20

Beta strand

485 – 490

6

Beta strand

492 – 494

3

Beta strand

504 – 506

3

Helix

510 – 521

12

Beta strand

525 – 527

3

Helix

528 – 530

3

Beta strand

534 – 536

3

Helix

540 – 552

13

Helix

554 – 556

3

Turn

557 – 560

4

Beta strand

561 – 565

5

Beta strand

570 – 573

4

Helix

574 – 586

13

Helix

591 – 593

3

Beta strand

600 – 602

3

Helix

606 – 609

4

Helix

624 – 630

7

Helix

638 – 652

15

Sequences

	Sequence		Length	Mass (Da)
	P77398 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: A430928AB4041FA3	FASTA	660	74,289
	10 20 30 40 50 60 MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA ERGIPVYAPD 70 80 90 100 110 120 NVNHPLWVER IAQLSPDVIF SFYYRHLIYD EILQLAPAGA FNLHGSLLPK YRGRAPLNWV 130 140 150 160 170 180 LVNGETETGV TLHRMVKRAD AGAIVAQLRI AIAPDDIAIT LHHKLCHAAR QLLEQTLPAI 190 200 210 220 230 240 KHGNILEIAQ RENEATCFGR RTPDDSFLEW HKPASVLHNM VRAVADPWPG AFSYVGNQKF 250 260 270 280 290 300 TVWSSRVHPH ASKAQPGSVI SVAPLLIACG DGALEIVTGQ AGDGITMQGS QLAQTLGLVQ 310 320 330 340 350 360 GSRLNSQPAC TARRRTRVLI LGVNGFIGNH LTERLLREDH YEVYGLDIGS DAISRFLNHP 370 380 390 400 410 420 HFHFVEGDIS IHSEWIEYHV KKCDVVLPLV AIATPIEYTR NPLRVFELDF EENLRIIRYC 430 440 450 460 470 480 VKYRKRIIFP STSEVYGMCS DKYFDEDHSN LIVGPVNKPR WIYSVSKQLL DRVIWAYGEK 490 500 510 520 530 540 EGLQFTLFRP FNWMGPRLDN LNAARIGSSR AITQLILNLV EGSPIKLIDG GKQKRCFTDI 550 560 570 580 590 600 RDGIEALYRI IENAGNRCDG EIINIGNPEN EASIEELGEM LLASFEKHPL RHHFPPFAGF 610 620 630 640 650 660 RVVESSSYYG KGYQDVEHRK PSIRNAHRCL DWEPKIDMQE TIDETLDFFL RTVDLTDKPS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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." Breazeale S.D., Ribeiro A.A., Raetz C.R.H. J. Biol. Chem. 277:2886-2896(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION OF C-TERMINAL DOMAIN, CHARACTERIZATION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes." Winfield M.D., Groisman E.A. Proc. Natl. Acad. Sci. U.S.A. 101:17162-17167(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION BY BASR. Strain: K12 / MG1655 / ATCC 47076.
[6]	"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." Breazeale S.D., Ribeiro A.A., McClerren A.L., Raetz C.R.H. J. Biol. Chem. 280:14154-14167(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF N-TERMINAL DOMAIN, CATALYTIC ACTIVITY, CHARACTERIZATION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli." Yan A., Guan Z., Raetz C.R.H. J. Biol. Chem. 282:36077-36089(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PATHWAY. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"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." Gatzeva-Topalova P.Z., May A.P., Sousa M.C. Biochemistry 43:13370-13379(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 306-660, CATALYTIC ACTIVITY OF C-TERMINAL DOMAIN, BIOPHYSICOCHEMICAL PROPERTIES.
[9]	"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." Gatzeva-Topalova P.Z., May A.P., Sousa M.C. Biochemistry 44:5328-5338(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-300, MUTAGENESIS OF ASN-102; HIS-104 AND ASP-140, REACTION MECHASNISM.
[10]	"Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis." Williams G.J., Breazeale S.D., Raetz C.R.H., Naismith J.H. J. Biol. Chem. 280:23000-23008(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) IN COMPLEX WITH UMP AND N-5-FTHF, MUTAGENESIS OF SER-433 AND GLU-434.
[11]	"Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance." Gatzeva-Topalova P.Z., May A.P., Sousa M.C. Structure 13:929-942(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) IN COMPLEX WITH UDP-GLCUA AND NAD ANALOG AND OF 306-660 OF MUTANTS ALA-433; GLU-619; MET-619 AND TYR-619, MUTAGENESIS OF SER-433 AND ARG-619, SUBUNIT, REACTION MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY057445 Genomic DNA. Translation: AAL23678.1.
U00096 Genomic DNA. Translation: AAC75315.1.
AP009048 Genomic DNA. Translation: BAA16078.1.

PIR

E64996.

RefSeq

NP_416758.1. NC_000913.2.
YP_490494.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U9J	X-ray	2.40	A	306-660	[»]
1YRW	X-ray	1.70	A	1-300	[»]
1Z73	X-ray	2.50	A	306-660	[»]
1Z74	X-ray	2.70	A	306-660	[»]
1Z75	X-ray	2.40	A	306-660	[»]
1Z7B	X-ray	2.31	A	306-660	[»]
1Z7E	X-ray	3.00	A/B/C/D/E/F	1-660	[»]
2BLL	X-ray	2.30	A	317-660	[»]
2BLN	X-ray	1.20	A/B	1-305	[»]

ProteinModelPortal

P77398.

SMR

P77398. Positions 1-656.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11961N.

IntAct

P77398. 12 interactions.

MINT

MINT-1257581.

STRING

511145.b2255.

Proteomic databases

PaxDb

P77398.

PRIDE

P77398.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75315; AAC75315; b2255.
BAA16078; BAA16078; BAA16078.

GeneID

12931503.
947683.

KEGG

ecj:Y75_p2218.
eco:b2255.

PATRIC

32119875. VBIEscCol129921_2347.

Organism-specific databases

EchoBASE

EB3844.

EcoGene

EG14091. arnA.

Phylogenomic databases

eggNOG

COG0451.

HOGENOM

HOG000247761.

KO

K10011.

OMA

VRYCVKY.

ProtClustDB

PRK08125.

Enzyme and pathway databases

BioCyc

EcoCyc:G7168-MONOMER.
ECOL316407:JW2249-MONOMER.
MetaCyc:G7168-MONOMER.

SABIO-RK

P77398.

UniPathway

UPA00030.
UPA00032; UER00492.
UPA00032; UER00494.

Gene expression databases

Genevestigator

P77398.

Family and domain databases

Gene3D

3.10.25.10. 1 hit.
3.40.50.170. 1 hit.
3.40.50.720. 1 hit.

HAMAP

MF_01166. ArnA.

InterPro

IPR021168. Bifun_polymyxin_resist_ArnA.
IPR001509. Epimerase_deHydtase.
IPR005793. Formyl_trans_C.
IPR002376. Formyl_transf_N.
IPR011034. Formyl_transferase_C-like.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF01370. Epimerase. 1 hit.
PF02911. Formyl_trans_C. 1 hit.
PF00551. Formyl_trans_N. 1 hit.
[Graphical view]

PIRSF

PIRSF036506. Bifun_polymyxin_resist_ArnA. 1 hit.

SUPFAM

SSF50486. FMT_C_like. 1 hit.
SSF53328. formyl_transf. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P77398.

Entry information

Entry name

ARNA_ECOLI

Accession

Primary (citable) accession number: P77398
Secondary accession number(s): Q56VX0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 124 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program