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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)DescriptionActionsGraphical viewLength
    Sitei102Transition state stabilizer1
    Active sitei104Proton donor; for formyltransferase activity1
    Binding sitei11410-formyltetrahydrofolate1
    Sitei140Raises pKa of active site His1
    Binding sitei347NAD1
    Binding sitei393UDP-glucuronate; via carbonyl oxygen1
    Binding sitei398UDP-glucuronate1
    Active sitei434Proton acceptor; for decarboxylase activity1
    Binding sitei460UDP-glucuronate1
    Binding sitei492UDP-glucuronate1
    Binding sitei613UDP-glucuronate1
    Active sitei619Proton donor; for decarboxylase activity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi368 – 369NAD binding2

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14091. arnA.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi102N → A: No activity. 1 Publication1
    Mutagenesisi104H → A: 25-fold lower activity. 1 Publication1
    Mutagenesisi104H → K: Less than 1% residual activity. 1 Publication1
    Mutagenesisi140D → A or N: Less than 1% residual activity. 1 Publication1
    Mutagenesisi433S → A: 40-fold lower specific activity. 2 Publications1
    Mutagenesisi433S → T: No activity. 2 Publications1
    Mutagenesisi434E → A: 100-fold lower specific activity. 1 Publication1
    Mutagenesisi434E → Q: No activity. 1 Publication1
    Mutagenesisi619R → E or Y: No activity. 1 Publication1
    Mutagenesisi619R → M: 400-fold lower activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000830981 – 660Bifunctional polymyxin resistance protein ArnAAdd BLAST660

    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 interactors.
    DIPiDIP-11961N.
    IntActiP77398. 14 interactors.
    MINTiMINT-1257581.
    STRINGi511145.b2255.

    Structurei

    Secondary structure

    1660
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 7Combined sources6
    Helixi9 – 21Combined sources13
    Beta strandi25 – 30Combined sources6
    Helixi45 – 52Combined sources8
    Helixi65 – 73Combined sources9
    Beta strandi77 – 83Combined sources7
    Helixi90 – 93Combined sources4
    Beta strandi100 – 106Combined sources7
    Turni108 – 111Combined sources4
    Beta strandi112 – 114Combined sources3
    Helixi116 – 122Combined sources7
    Beta strandi126 – 134Combined sources9
    Turni139 – 141Combined sources3
    Beta strandi144 – 151Combined sources8
    Helixi158 – 181Combined sources24
    Helixi192 – 194Combined sources3
    Helixi203 – 206Combined sources4
    Helixi214 – 223Combined sources10
    Beta strandi231 – 235Combined sources5
    Beta strandi238 – 248Combined sources11
    Beta strandi258 – 261Combined sources4
    Turni262 – 264Combined sources3
    Beta strandi265 – 268Combined sources4
    Beta strandi270 – 281Combined sources12
    Helixi289 – 296Combined sources8
    Beta strandi299 – 301Combined sources3
    Beta strandi317 – 322Combined sources6
    Helixi326 – 337Combined sources12
    Beta strandi342 – 348Combined sources7
    Helixi351 – 356Combined sources6
    Beta strandi362 – 366Combined sources5
    Turni369 – 371Combined sources3
    Helixi374 – 382Combined sources9
    Beta strandi384 – 388Combined sources5
    Helixi395 – 400Combined sources6
    Helixi402 – 409Combined sources8
    Helixi411 – 422Combined sources12
    Beta strandi426 – 430Combined sources5
    Helixi433 – 436Combined sources4
    Beta strandi442 – 444Combined sources3
    Turni446 – 448Combined sources3
    Beta strandi451 – 453Combined sources3
    Helixi459 – 461Combined sources3
    Helixi462 – 481Combined sources20
    Beta strandi485 – 490Combined sources6
    Beta strandi492 – 494Combined sources3
    Beta strandi504 – 506Combined sources3
    Helixi510 – 521Combined sources12
    Beta strandi525 – 527Combined sources3
    Helixi528 – 530Combined sources3
    Beta strandi534 – 536Combined sources3
    Helixi540 – 552Combined sources13
    Helixi554 – 556Combined sources3
    Turni557 – 560Combined sources4
    Beta strandi561 – 565Combined sources5
    Beta strandi570 – 573Combined sources4
    Helixi574 – 586Combined sources13
    Helixi591 – 593Combined sources3
    Beta strandi600 – 602Combined sources3
    Helixi606 – 609Combined sources4
    Helixi624 – 630Combined sources7
    Helixi638 – 652Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77398.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni1 – 304Formyltransferase ArnAFTAdd BLAST304
    Regioni86 – 8810-formyltetrahydrofolate binding3
    Regioni136 – 14010-formyltetrahydrofolate binding5
    Regioni314 – 660Dehydrogenase ArnADHAdd BLAST347
    Regioni432 – 433UDP-glucuronate binding2
    Regioni526 – 535UDP-glucuronate binding10

    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.
    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260497. 240 interactors.
    DIPiDIP-11961N.
    IntActiP77398. 14 interactors.
    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.
    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: November 30, 2016
    This is version 153 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.