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Protein

Ornithine carbamoyltransferase, catabolic

Gene

arcB

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline.1 Publication

Catalytic activityi

Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.

Enzyme regulationi

Inhibited by 2-aminopentanoic acid (norvaline).1 Publication

Kineticsi

  1. KM=0.32 mM for carbamoyl phosphate (at pH 6.8 and 37 degrees Celsius)1 Publication
  2. KM=0.22 mM for L-ornithine (at pH 6.8 and 37 degrees Celsius)1 Publication

    Pathwayi: L-arginine degradation via ADI pathway

    This protein is involved in step 2 of the subpathway that synthesizes carbamoyl phosphate from L-arginine.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Arginine deiminase (arcA)
    2. Ornithine carbamoyltransferase, catabolic (arcB)
    This subpathway is part of the pathway L-arginine degradation via ADI pathway, which is itself part of Amino-acid degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes carbamoyl phosphate from L-arginine, the pathway L-arginine degradation via ADI pathway and in Amino-acid degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei33 – 331Carbamoyl phosphate
    Binding sitei73 – 731Carbamoyl phosphateBy similarity
    Binding sitei84 – 841Carbamoyl phosphateBy similarity
    Binding sitei108 – 1081Carbamoyl phosphateBy similarity
    Binding sitei168 – 1681OrnithineBy similarity
    Binding sitei232 – 2321OrnithineBy similarity
    Binding sitei303 – 3031Carbamoyl phosphateBy similarity
    Binding sitei321 – 3211Carbamoyl phosphateBy similarity

    GO - Molecular functioni

    • amino acid binding Source: InterPro
    • ornithine carbamoyltransferase activity Source: PseudoCAP

    GO - Biological processi

    • arginine biosynthetic process via ornithine Source: GO_Central
    • arginine catabolic process to ornithine Source: UniProtKB-UniPathway
    • arginine deiminase pathway Source: PseudoCAP
    • urea cycle Source: GO_Central
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Arginine metabolism

    Enzyme and pathway databases

    SABIO-RKP08308.
    UniPathwayiUPA00254; UER00365.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ornithine carbamoyltransferase, catabolic (EC:2.1.3.3)
    Short name:
    OTCase
    Gene namesi
    Name:arcB
    Ordered Locus Names:PA5172
    OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Taxonomic identifieri208964 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    Proteomesi
    • UP000002438 Componenti: Chromosome

    Organism-specific databases

    PseudoCAPiPA5172.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi106 – 1061E → A or G: Loss of homotropic cooperativity; gain of anabolic activity. Conformational change which modifies the catalytic site. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved
    Chaini2 – 336335Ornithine carbamoyltransferase, catabolicPRO_0000112986Add
    BLAST

    Proteomic databases

    PaxDbiP08308.

    Interactioni

    Subunit structurei

    Dodecamer (tetramer of trimers).2 Publications

    Protein-protein interaction databases

    STRINGi208964.PA5172.

    Structurei

    Secondary structure

    1
    336
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 134Combined sources
    Helixi18 – 3619Combined sources
    Beta strandi48 – 558Combined sources
    Helixi58 – 7013Combined sources
    Beta strandi74 – 785Combined sources
    Turni80 – 823Combined sources
    Turni85 – 873Combined sources
    Helixi91 – 10111Combined sources
    Beta strandi103 – 1086Combined sources
    Helixi112 – 12110Combined sources
    Beta strandi122 – 1243Combined sources
    Beta strandi126 – 1305Combined sources
    Helixi136 – 14813Combined sources
    Helixi154 – 1563Combined sources
    Beta strandi158 – 1636Combined sources
    Helixi168 – 17912Combined sources
    Beta strandi183 – 1875Combined sources
    Helixi190 – 1923Combined sources
    Helixi196 – 20914Combined sources
    Beta strandi212 – 2176Combined sources
    Helixi219 – 2224Combined sources
    Turni223 – 2253Combined sources
    Beta strandi227 – 2315Combined sources
    Beta strandi237 – 2393Combined sources
    Helixi241 – 2433Combined sources
    Helixi245 – 2517Combined sources
    Helixi252 – 2543Combined sources
    Helixi258 – 2625Combined sources
    Beta strandi270 – 2734Combined sources
    Beta strandi280 – 2834Combined sources
    Helixi284 – 2929Combined sources
    Helixi294 – 2985Combined sources
    Beta strandi299 – 3035Combined sources
    Helixi304 – 3074Combined sources
    Beta strandi309 – 3124Combined sources
    Helixi314 – 33320Combined sources

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei32 – 321Important for structural integrity
    Sitei148 – 1481Important for structural integrity

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DXHX-ray2.50A2-336[»]
    1ORTX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L2-336[»]
    ProteinModelPortaliP08308.
    SMRiP08308. Positions 2-336.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08308.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 166Carbamoyl phosphate binding
    Regioni57 – 615Carbamoyl phosphate bindingBy similarity
    Regioni135 – 1384Carbamoyl phosphate bindingBy similarity
    Regioni236 – 2372Ornithine bindingBy similarity
    Regioni273 – 2764Carbamoyl phosphate bindingBy similarity

    Sequence similaritiesi

    Belongs to the ATCase/OTCase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DBV. Bacteria.
    COG0078. LUCA.
    HOGENOMiHOG000022686.
    InParanoidiP08308.
    KOiK00611.
    OMAiMGMEIRL.
    OrthoDBiEOG690MGV.
    PhylomeDBiP08308.

    Family and domain databases

    Gene3Di3.40.50.1370. 2 hits.
    HAMAPiMF_01109. OTCase.
    InterProiIPR006132. Asp/Orn_carbamoyltranf_P-bd.
    IPR006130. Asp/Orn_carbamoylTrfase.
    IPR006131. Asp_carbamoyltransf_Asp/Orn-bd.
    IPR002292. Orn/put_carbamltrans.
    IPR024904. OTCase_ArgI.
    [Graphical view]
    PfamiPF00185. OTCace. 1 hit.
    PF02729. OTCace_N. 1 hit.
    [Graphical view]
    PRINTSiPR00100. AOTCASE.
    PR00102. OTCASE.
    SUPFAMiSSF53671. SSF53671. 1 hit.
    TIGRFAMsiTIGR00658. orni_carb_tr. 1 hit.
    PROSITEiPS00097. CARBAMOYLTRANSFERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P08308-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAFNMHNRNL LSLMHHSTRE LRYLLDLSRD LKRAKYTGTE QQHLKRKNIA
    60 70 80 90 100
    LIFEKTSTRT RCAFEVAAYD QGANVTYIDP NSSQIGHKES MKDTARVLGR
    110 120 130 140 150
    MYDAIEYRGF KQEIVEELAK FAGVPVFNGL TDEYHPTQML ADVLTMREHS
    160 170 180 190 200
    DKPLHDISYA YLGDARNNMG NSLLLIGAKL GMDVRIAAPK ALWPHDEFVA
    210 220 230 240 250
    QCKKFAEESG AKLTLTEDPK EAVKGVDFVH TDVWVSMGEP VEAWGERIKE
    260 270 280 290 300
    LLPYQVNMEI MKATGNPRAK FMHCLPAFHN SETKVGKQIA EQYPNLANGI
    310 320 330
    EVTEDVFESP YNIAFEQAEN RMHTIKAILV STLADI
    Length:336
    Mass (Da):38,109
    Last modified:January 23, 2007 - v3
    Checksum:i4E780414EADA4724
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X05637 Genomic DNA. Translation: CAA29124.1.
    AE004091 Genomic DNA. Translation: AAG08557.1.
    PIRiS00032. OWPSCA.
    RefSeqiNP_253859.1. NC_002516.2.
    WP_003100031.1. NZ_ASJY01000811.1.

    Genome annotation databases

    EnsemblBacteriaiAAG08557; AAG08557; PA5172.
    GeneIDi881792.
    KEGGipae:PA5172.
    PATRICi19845187. VBIPseAer58763_5420.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X05637 Genomic DNA. Translation: CAA29124.1.
    AE004091 Genomic DNA. Translation: AAG08557.1.
    PIRiS00032. OWPSCA.
    RefSeqiNP_253859.1. NC_002516.2.
    WP_003100031.1. NZ_ASJY01000811.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DXHX-ray2.50A2-336[»]
    1ORTX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L2-336[»]
    ProteinModelPortaliP08308.
    SMRiP08308. Positions 2-336.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi208964.PA5172.

    Proteomic databases

    PaxDbiP08308.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAG08557; AAG08557; PA5172.
    GeneIDi881792.
    KEGGipae:PA5172.
    PATRICi19845187. VBIPseAer58763_5420.

    Organism-specific databases

    PseudoCAPiPA5172.

    Phylogenomic databases

    eggNOGiENOG4105DBV. Bacteria.
    COG0078. LUCA.
    HOGENOMiHOG000022686.
    InParanoidiP08308.
    KOiK00611.
    OMAiMGMEIRL.
    OrthoDBiEOG690MGV.
    PhylomeDBiP08308.

    Enzyme and pathway databases

    UniPathwayiUPA00254; UER00365.
    SABIO-RKP08308.

    Miscellaneous databases

    EvolutionaryTraceiP08308.

    Family and domain databases

    Gene3Di3.40.50.1370. 2 hits.
    HAMAPiMF_01109. OTCase.
    InterProiIPR006132. Asp/Orn_carbamoyltranf_P-bd.
    IPR006130. Asp/Orn_carbamoylTrfase.
    IPR006131. Asp_carbamoyltransf_Asp/Orn-bd.
    IPR002292. Orn/put_carbamltrans.
    IPR024904. OTCase_ArgI.
    [Graphical view]
    PfamiPF00185. OTCace. 1 hit.
    PF02729. OTCace_N. 1 hit.
    [Graphical view]
    PRINTSiPR00100. AOTCASE.
    PR00102. OTCASE.
    SUPFAMiSSF53671. SSF53671. 1 hit.
    TIGRFAMsiTIGR00658. orni_carb_tr. 1 hit.
    PROSITEiPS00097. CARBAMOYLTRANSFERASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Primary and quaternary structure of the catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Extensive sequence homology with the anabolic ornithine carbamoyltransferases of Escherichia coli."
      Baur H., Stalon V., Falmagne P., Luethi E., Haas D.
      Eur. J. Biochem. 166:111-117(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: PAO.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
    3. "The occurrence of a catabolic and an anabolic ornithine carbamoyltransferase in Pseudomonas."
      Stalon V., Ramos F., Pierard A., Wiame J.M.
      Biochim. Biophys. Acta 139:91-97(1967) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A CATABOLIC OTCASE.
    4. "Converting catabolic ornithine carbamoyltransferase to an anabolic enzyme."
      Baur H., Tricot C., Stalon V., Haas D.
      J. Biol. Chem. 265:14728-14731(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLU-106.
    5. "Steady-state kinetics and analysis of pH dependence on wild-type and a modified allosteric Pseudomonas aeruginosa ornithine carbamoyltransferase containing the replacement of glutamate 105 by alanine."
      Tricot C., Nguyen V.T., Stalon V.
      Eur. J. Biochem. 215:833-839(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLU-106, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
    6. "Purification, crystallization and preliminary X-ray analysis of catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa."
      Sainz G., Vicat J., Kahn R., Tricot C., Stalon V., Dideberg O.
      Acta Crystallogr. D 55:1591-1593(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    7. "Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0-A resolution: a different oligomeric organization in the transcarbamoylase family."
      Villeret V., Tricot C., Stalon V., Dideberg O.
      Proc. Natl. Acad. Sci. U.S.A. 92:10762-10766(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
    8. "Catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa."
      Sainz G., Vicat J., Kahn R., Duee E., Tricot C., Stalon V., Dideberg O.
      Submitted (JAN-2000) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF MUTANT GLY-106, SUBUNIT.

    Entry informationi

    Entry nameiOTCC_PSEAE
    AccessioniPrimary (citable) accession number: P08308
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: January 23, 2007
    Last modified: February 17, 2016
    This is version 139 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Proceeds by an ordered sequential mechanism with CP identified as the initial reactant.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.