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Protein

Bifunctional polymyxin resistance protein ArnA

Gene

arnA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

UDP-alpha-D-glucuronate + NAD+ = UDP-beta-L-threo-pentapyranos-4-ulose + CO2 + NADH.
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose.

Kineticsi

  1. KM=0.76 mM for NAD1 Publication
  2. KM=0.086 mM for UDP-GlcUA1 Publication

    Pathwayi: UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis

    This protein is involved in step 1 and 3 of the subpathway that synthesizes UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate.1 Publication
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Bifunctional polymyxin resistance protein ArnA (arnA)
    2. UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase (arnB)
    3. Bifunctional polymyxin resistance protein ArnA (arnA)
    This subpathway is part of the pathway UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis, which is itself part of Nucleotide-sugar biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate, the pathway UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis and in Nucleotide-sugar biosynthesis.

    Pathwayi: lipopolysaccharide biosynthesis

    This protein is involved in the pathway lipopolysaccharide biosynthesis, which is part of Bacterial outer membrane biogenesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway lipopolysaccharide biosynthesis and in Bacterial outer membrane biogenesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei102 – 1021Transition state stabilizer
    Active sitei104 – 1041Proton donor; for formyltransferase activity
    Binding sitei114 – 114110-formyltetrahydrofolate
    Sitei140 – 1401Raises pKa of active site His
    Binding sitei347 – 3471NAD
    Binding sitei393 – 3931UDP-glucuronate; via carbonyl oxygen
    Binding sitei398 – 3981UDP-glucuronate
    Active sitei434 – 4341Proton acceptor; for decarboxylase activity
    Binding sitei460 – 4601UDP-glucuronate
    Binding sitei492 – 4921UDP-glucuronate
    Binding sitei613 – 6131UDP-glucuronate
    Active sitei619 – 6191Proton donor; for decarboxylase activity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi368 – 3692NAD binding

    GO - Molecular functioni

    GO - Biological processi

    • lipid A biosynthetic process Source: EcoCyc
    • lipopolysaccharide biosynthetic process Source: UniProtKB-UniPathway
    • response to antibiotic Source: EcoCyc
    • UDP-D-xylose biosynthetic process Source: UniProtKB

    Keywords - Molecular functioni

    Oxidoreductase, Transferase

    Keywords - Biological processi

    Antibiotic resistance, Lipid A biosynthesis, Lipid biosynthesis, Lipid metabolism, Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciEcoCyc:G7168-MONOMER.
    ECOL316407:JW2249-MONOMER.
    MetaCyc:G7168-MONOMER.
    BRENDAi1.1.1.305. 2026.
    2.1.2.13. 2026.
    SABIO-RKP77398.
    UniPathwayiUPA00030.
    UPA00032; UER00492.
    UPA00032; UER00494.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Bifunctional polymyxin resistance protein ArnA
    Alternative name(s):
    Polymyxin resistance protein PmrI
    Including the following 2 domains:
    UDP-4-amino-4-deoxy-L-arabinose formyltransferase (EC:2.1.2.13)
    Alternative name(s):
    ArnAFT
    UDP-L-Ara4N formyltransferase
    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 namesi
    Name:arnA
    Synonyms:pmrI, yfbG
    Ordered Locus Names:b2255, JW2249
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14091. arnA.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi102 – 1021N → A: No activity. 1 Publication
    Mutagenesisi104 – 1041H → A: 25-fold lower activity. 1 Publication
    Mutagenesisi104 – 1041H → K: Less than 1% residual activity. 1 Publication
    Mutagenesisi140 – 1401D → A or N: Less than 1% residual activity. 1 Publication
    Mutagenesisi433 – 4331S → A: 40-fold lower specific activity. 2 Publications
    Mutagenesisi433 – 4331S → T: No activity. 2 Publications
    Mutagenesisi434 – 4341E → A: 100-fold lower specific activity. 1 Publication
    Mutagenesisi434 – 4341E → Q: No activity. 1 Publication
    Mutagenesisi619 – 6191R → E or Y: No activity. 1 Publication
    Mutagenesisi619 – 6191R → M: 400-fold lower activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 660660Bifunctional polymyxin resistance protein ArnAPRO_0000083098Add
    BLAST

    Proteomic databases

    EPDiP77398.
    PaxDbiP77398.
    PRIDEiP77398.

    Expressioni

    Inductioni

    Induced by BasR.1 Publication

    Interactioni

    Subunit structurei

    Homohexamer, formed by a dimer of trimers.2 Publications

    Protein-protein interaction databases

    BioGridi4260497. 240 interactions.
    DIPiDIP-11961N.
    IntActiP77398. 14 interactions.
    MINTiMINT-1257581.
    STRINGi511145.b2255.

    Structurei

    Secondary structure

    1
    660
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76Combined sources
    Helixi9 – 2113Combined sources
    Beta strandi25 – 306Combined sources
    Helixi45 – 528Combined sources
    Helixi65 – 739Combined sources
    Beta strandi77 – 837Combined sources
    Helixi90 – 934Combined sources
    Beta strandi100 – 1067Combined sources
    Turni108 – 1114Combined sources
    Beta strandi112 – 1143Combined sources
    Helixi116 – 1227Combined sources
    Beta strandi126 – 1349Combined sources
    Turni139 – 1413Combined sources
    Beta strandi144 – 1518Combined sources
    Helixi158 – 18124Combined sources
    Helixi192 – 1943Combined sources
    Helixi203 – 2064Combined sources
    Helixi214 – 22310Combined sources
    Beta strandi231 – 2355Combined sources
    Beta strandi238 – 24811Combined sources
    Beta strandi258 – 2614Combined sources
    Turni262 – 2643Combined sources
    Beta strandi265 – 2684Combined sources
    Beta strandi270 – 28112Combined sources
    Helixi289 – 2968Combined sources
    Beta strandi299 – 3013Combined sources
    Beta strandi317 – 3226Combined sources
    Helixi326 – 33712Combined sources
    Beta strandi342 – 3487Combined sources
    Helixi351 – 3566Combined sources
    Beta strandi362 – 3665Combined sources
    Turni369 – 3713Combined sources
    Helixi374 – 3829Combined sources
    Beta strandi384 – 3885Combined sources
    Helixi395 – 4006Combined sources
    Helixi402 – 4098Combined sources
    Helixi411 – 42212Combined sources
    Beta strandi426 – 4305Combined sources
    Helixi433 – 4364Combined sources
    Beta strandi442 – 4443Combined sources
    Turni446 – 4483Combined sources
    Beta strandi451 – 4533Combined sources
    Helixi459 – 4613Combined sources
    Helixi462 – 48120Combined sources
    Beta strandi485 – 4906Combined sources
    Beta strandi492 – 4943Combined sources
    Beta strandi504 – 5063Combined sources
    Helixi510 – 52112Combined sources
    Beta strandi525 – 5273Combined sources
    Helixi528 – 5303Combined sources
    Beta strandi534 – 5363Combined sources
    Helixi540 – 55213Combined sources
    Helixi554 – 5563Combined sources
    Turni557 – 5604Combined sources
    Beta strandi561 – 5655Combined sources
    Beta strandi570 – 5734Combined sources
    Helixi574 – 58613Combined sources
    Helixi591 – 5933Combined sources
    Beta strandi600 – 6023Combined sources
    Helixi606 – 6094Combined sources
    Helixi624 – 6307Combined sources
    Helixi638 – 65215Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1U9JX-ray2.40A306-660[»]
    1YRWX-ray1.70A1-300[»]
    1Z73X-ray2.50A306-660[»]
    1Z74X-ray2.70A306-660[»]
    1Z75X-ray2.40A306-660[»]
    1Z7BX-ray2.31A306-660[»]
    1Z7EX-ray3.00A/B/C/D/E/F1-660[»]
    2BLLX-ray2.30A317-660[»]
    2BLNX-ray1.20A/B1-305[»]
    4WKGX-ray2.70A/B/C/D/E/F1-660[»]
    ProteinModelPortaliP77398.
    SMRiP77398. Positions 1-656.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77398.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 304304Formyltransferase ArnAFTAdd
    BLAST
    Regioni86 – 88310-formyltetrahydrofolate binding
    Regioni136 – 140510-formyltetrahydrofolate binding
    Regioni314 – 660347Dehydrogenase ArnADHAdd
    BLAST
    Regioni432 – 4332UDP-glucuronate binding
    Regioni526 – 53510UDP-glucuronate binding

    Sequence similaritiesi

    In the N-terminal section; belongs to the Fmt family. UDP-L-Ara4N formyltransferase subfamily.Curated

    Phylogenomic databases

    eggNOGiENOG4105C3I. Bacteria.
    COG0223. LUCA.
    COG0451. LUCA.
    HOGENOMiHOG000247761.
    InParanoidiP77398.
    KOiK10011.
    OMAiVRYCVKY.
    PhylomeDBiP77398.

    Family and domain databases

    Gene3Di3.10.25.10. 1 hit.
    3.40.50.170. 1 hit.
    3.40.50.720. 1 hit.
    HAMAPiMF_01166. ArnA. 1 hit.
    InterProiIPR021168. Bifun_polymyxin_resist_ArnA.
    IPR001509. Epimerase_deHydtase_N.
    IPR005793. Formyl_trans_C.
    IPR002376. Formyl_transf_N.
    IPR011034. Formyl_transferase_C-like.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF01370. Epimerase. 1 hit.
    PF02911. Formyl_trans_C. 1 hit.
    PF00551. Formyl_trans_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF036506. Bifun_polymyxin_resist_ArnA. 1 hit.
    SUPFAMiSSF50486. SSF50486. 1 hit.
    SSF51735. SSF51735. 1 hit.
    SSF53328. SSF53328. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P77398-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA
    60 70 80 90 100
    ERGIPVYAPD NVNHPLWVER IAQLSPDVIF SFYYRHLIYD EILQLAPAGA
    110 120 130 140 150
    FNLHGSLLPK YRGRAPLNWV LVNGETETGV TLHRMVKRAD AGAIVAQLRI
    160 170 180 190 200
    AIAPDDIAIT LHHKLCHAAR QLLEQTLPAI KHGNILEIAQ RENEATCFGR
    210 220 230 240 250
    RTPDDSFLEW HKPASVLHNM VRAVADPWPG AFSYVGNQKF TVWSSRVHPH
    260 270 280 290 300
    ASKAQPGSVI SVAPLLIACG DGALEIVTGQ AGDGITMQGS QLAQTLGLVQ
    310 320 330 340 350
    GSRLNSQPAC TARRRTRVLI LGVNGFIGNH LTERLLREDH YEVYGLDIGS
    360 370 380 390 400
    DAISRFLNHP HFHFVEGDIS IHSEWIEYHV KKCDVVLPLV AIATPIEYTR
    410 420 430 440 450
    NPLRVFELDF EENLRIIRYC VKYRKRIIFP STSEVYGMCS DKYFDEDHSN
    460 470 480 490 500
    LIVGPVNKPR WIYSVSKQLL DRVIWAYGEK EGLQFTLFRP FNWMGPRLDN
    510 520 530 540 550
    LNAARIGSSR AITQLILNLV EGSPIKLIDG GKQKRCFTDI RDGIEALYRI
    560 570 580 590 600
    IENAGNRCDG EIINIGNPEN EASIEELGEM LLASFEKHPL RHHFPPFAGF
    610 620 630 640 650
    RVVESSSYYG KGYQDVEHRK PSIRNAHRCL DWEPKIDMQE TIDETLDFFL
    660
    RTVDLTDKPS
    Length:660
    Mass (Da):74,289
    Last modified:February 1, 1997 - v1
    Checksum:iA430928AB4041FA3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY057445 Genomic DNA. Translation: AAL23678.1.
    U00096 Genomic DNA. Translation: AAC75315.1.
    AP009048 Genomic DNA. Translation: BAA16078.1.
    PIRiE64996.
    RefSeqiNP_416758.1. NC_000913.3.
    WP_000860273.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75315; AAC75315; b2255.
    BAA16078; BAA16078; BAA16078.
    GeneIDi947683.
    KEGGiecj:JW2249.
    eco:b2255.
    PATRICi32119875. VBIEscCol129921_2347.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY057445 Genomic DNA. Translation: AAL23678.1.
    U00096 Genomic DNA. Translation: AAC75315.1.
    AP009048 Genomic DNA. Translation: BAA16078.1.
    PIRiE64996.
    RefSeqiNP_416758.1. NC_000913.3.
    WP_000860273.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1U9JX-ray2.40A306-660[»]
    1YRWX-ray1.70A1-300[»]
    1Z73X-ray2.50A306-660[»]
    1Z74X-ray2.70A306-660[»]
    1Z75X-ray2.40A306-660[»]
    1Z7BX-ray2.31A306-660[»]
    1Z7EX-ray3.00A/B/C/D/E/F1-660[»]
    2BLLX-ray2.30A317-660[»]
    2BLNX-ray1.20A/B1-305[»]
    4WKGX-ray2.70A/B/C/D/E/F1-660[»]
    ProteinModelPortaliP77398.
    SMRiP77398. Positions 1-656.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260497. 240 interactions.
    DIPiDIP-11961N.
    IntActiP77398. 14 interactions.
    MINTiMINT-1257581.
    STRINGi511145.b2255.

    Proteomic databases

    EPDiP77398.
    PaxDbiP77398.
    PRIDEiP77398.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75315; AAC75315; b2255.
    BAA16078; BAA16078; BAA16078.
    GeneIDi947683.
    KEGGiecj:JW2249.
    eco:b2255.
    PATRICi32119875. VBIEscCol129921_2347.

    Organism-specific databases

    EchoBASEiEB3844.
    EcoGeneiEG14091. arnA.

    Phylogenomic databases

    eggNOGiENOG4105C3I. Bacteria.
    COG0223. LUCA.
    COG0451. LUCA.
    HOGENOMiHOG000247761.
    InParanoidiP77398.
    KOiK10011.
    OMAiVRYCVKY.
    PhylomeDBiP77398.

    Enzyme and pathway databases

    UniPathwayiUPA00030.
    UPA00032; UER00492.
    UPA00032; UER00494.
    BioCyciEcoCyc:G7168-MONOMER.
    ECOL316407:JW2249-MONOMER.
    MetaCyc:G7168-MONOMER.
    BRENDAi1.1.1.305. 2026.
    2.1.2.13. 2026.
    SABIO-RKP77398.

    Miscellaneous databases

    EvolutionaryTraceiP77398.
    PROiP77398.

    Family and domain databases

    Gene3Di3.10.25.10. 1 hit.
    3.40.50.170. 1 hit.
    3.40.50.720. 1 hit.
    HAMAPiMF_01166. ArnA. 1 hit.
    InterProiIPR021168. Bifun_polymyxin_resist_ArnA.
    IPR001509. Epimerase_deHydtase_N.
    IPR005793. Formyl_trans_C.
    IPR002376. Formyl_transf_N.
    IPR011034. Formyl_transferase_C-like.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF01370. Epimerase. 1 hit.
    PF02911. Formyl_trans_C. 1 hit.
    PF00551. Formyl_trans_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF036506. Bifun_polymyxin_resist_ArnA. 1 hit.
    SUPFAMiSSF50486. SSF50486. 1 hit.
    SSF51735. SSF51735. 1 hit.
    SSF53328. SSF53328. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiARNA_ECOLI
    AccessioniPrimary (citable) accession number: P77398
    Secondary accession number(s): Q56VX0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: February 1, 1997
    Last modified: September 7, 2016
    This is version 151 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.