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Protein

D-ornithine 4,5-aminomutase subunit beta

Gene

oraE

Organism
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of a complex that catalyzes the reversible migration of the omega amino group of D-ornithine to C-4 to form (2R,4S)-2,4-diaminopentanoic acid. OraE may be the catalytic subunit. Active only on D-ornithine and 2,4-diaminopentanoic acid but not active on L-ornithine, L-beta-lysine, L-alpha-lysine or D-alpha-lysine.3 Publications

Catalytic activityi

D-ornithine = (2R,4S)-2,4-diaminopentanoate.3 Publications

Cofactori

Protein has several cofactor binding sites:
  • adenosylcob(III)alamin4 Publications
  • pyridoxal 5'-phosphate4 Publications

Enzyme regulationi

Increased activity in the presence of dithiothreitol (DTT) in vitro. Inhibited by 1 mM potassium phosphate and potassium chloride. Inhibited by L-alpha-ornithine, D,L-alpha-lysine, L-beta-lysine (50%-60%), L-alpha-lysine (26%) and by delta-amino-n-valeric acid to a lesser extent. Significant decrease in activity is observed in the presence of 0.2 mM p-chloromercuribenzoate, N-ethylmaleimide and also by 2 mM iodoacetate to a lesser extent but not inhibited by arsenite.2 Publications

Kineticsi

kcat is 6.3 sec(-1). Values are measured for recombinant S and E components expressed together in E.coli to overcome the presence of corrinoids in native system.

  1. KM=44.5 µM for D-ornithine3 Publications
  2. KM=0.43 µM for adenosylcobalamin3 Publications
  3. KM=1.5 µM for pyridoxal phosphate3 Publications

    pH dependencei

    Optimum pH is 9.0 or between 8.5-8.7 (with Tris-HCl buffer). Half-maximal activity is observed at pH 7.4 and 9.7.3 Publications

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius for native enzyme. Displays half-maximal activity at 23 degrees Celsius and 49 degrees Celsius. Rapidly inactivated at temperatures above 45 degrees Celsius. Loses more than 35% and 30% of its activity when stored at -20 degrees Celsius for 1 month and at 4 degrees Celsius for 48 hours, respectively.3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei81 – 811Substrate1 Publication
    Binding sitei160 – 1601Substrate
    Binding sitei182 – 1821Substrate1 Publication
    Metal bindingi615 – 6151Cobalt (adenosylcobalamin axial ligand); via tele nitrogen1 Publication
    Binding sitei700 – 7001Adenosylcobalamin
    Binding sitei720 – 7201Adenosylcobalamin

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Ligandi

    Cobalamin, Cobalt, Metal-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciCSTI499177:GJE9-1338-MONOMER.
    BRENDAi5.4.3.5. 13741.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-ornithine 4,5-aminomutase subunit beta (EC:5.4.3.53 Publications)
    Alternative name(s):
    D-ornithine aminomutase E component1 Publication
    Short name:
    OAM-E
    Gene namesi
    Name:oraE
    Ordered Locus Names:CLOST_1290
    OrganismiClostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
    Taxonomic identifieri499177 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaePeptoclostridium
    Proteomesi
    • UP000007041 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi615 – 6151H → G: Loss of corrinoid-binding ability. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 740740D-ornithine 4,5-aminomutase subunit betaPRO_0000421805Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei626 – 6261N6-(pyridoxal phosphate)lysine1 Publication

    Interactioni

    Subunit structurei

    Heterotetramer of 2 alpha (OraS) and 2 beta (OraE) subunits.3 Publications

    Protein-protein interaction databases

    STRINGi499177.CLOST_1290.

    Structurei

    Secondary structure

    1
    740
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi15 – 184Combined sources
    Turni19 – 213Combined sources
    Helixi22 – 243Combined sources
    Beta strandi41 – 433Combined sources
    Beta strandi46 – 527Combined sources
    Helixi62 – 676Combined sources
    Beta strandi73 – 819Combined sources
    Helixi87 – 9913Combined sources
    Beta strandi104 – 1063Combined sources
    Helixi113 – 1153Combined sources
    Beta strandi127 – 1304Combined sources
    Helixi134 – 15118Combined sources
    Beta strandi156 – 1605Combined sources
    Helixi166 – 17611Combined sources
    Beta strandi180 – 1823Combined sources
    Helixi185 – 1928Combined sources
    Helixi196 – 21217Combined sources
    Beta strandi216 – 2183Combined sources
    Helixi222 – 2276Combined sources
    Beta strandi228 – 2303Combined sources
    Helixi231 – 2333Combined sources
    Helixi235 – 25218Combined sources
    Helixi256 – 2583Combined sources
    Beta strandi259 – 2635Combined sources
    Helixi273 – 28715Combined sources
    Turni288 – 2903Combined sources
    Beta strandi291 – 2955Combined sources
    Helixi306 – 32217Combined sources
    Beta strandi326 – 3283Combined sources
    Turni333 – 3375Combined sources
    Helixi342 – 35817Combined sources
    Turni359 – 3613Combined sources
    Helixi362 – 3643Combined sources
    Beta strandi366 – 3683Combined sources
    Beta strandi370 – 3723Combined sources
    Helixi373 – 39422Combined sources
    Helixi398 – 4036Combined sources
    Turni430 – 4323Combined sources
    Beta strandi445 – 4473Combined sources
    Helixi455 – 4584Combined sources
    Helixi459 – 4613Combined sources
    Helixi465 – 4695Combined sources
    Turni473 – 4753Combined sources
    Helixi477 – 4793Combined sources
    Beta strandi488 – 4914Combined sources
    Helixi492 – 4987Combined sources
    Helixi499 – 5024Combined sources
    Beta strandi512 – 5143Combined sources
    Beta strandi519 – 52810Combined sources
    Helixi530 – 54314Combined sources
    Beta strandi547 – 55812Combined sources
    Turni559 – 5613Combined sources
    Beta strandi562 – 5709Combined sources
    Helixi577 – 5793Combined sources
    Helixi591 – 60010Combined sources
    Beta strandi604 – 6107Combined sources
    Helixi617 – 6215Combined sources
    Turni625 – 6284Combined sources
    Helixi630 – 6334Combined sources
    Beta strandi636 – 6394Combined sources
    Beta strandi642 – 6443Combined sources
    Helixi646 – 65510Combined sources
    Beta strandi659 – 6646Combined sources
    Helixi669 – 6713Combined sources
    Helixi672 – 68615Combined sources
    Turni690 – 6923Combined sources
    Beta strandi693 – 6986Combined sources
    Helixi704 – 7085Combined sources
    Turni709 – 7113Combined sources
    Beta strandi713 – 7164Combined sources
    Helixi722 – 73615Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3KOWX-ray2.90A/B/C/D1-740[»]
    3KOXX-ray2.40A/B/C/D1-740[»]
    3KOYX-ray2.80A/B/C/D1-740[»]
    3KOZX-ray2.80A/B/C/D1-740[»]
    3KP0X-ray2.80A/B/C/D1-740[»]
    3KP1X-ray2.01A/B/C/D1-740[»]
    ProteinModelPortaliE3PY95.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini602 – 739138B12-bindingPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni294 – 2963Substrate binding
    Regioni614 – 6163Adenosylcobalamin binding1 Publication
    Regioni664 – 6696Adenosylcobalamin binding1 Publication

    Sequence similaritiesi

    Contains 1 B12-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105EQ5. Bacteria.
    ENOG410XSK3. LUCA.
    HOGENOMiHOG000292273.
    KOiK17898.
    OMAiVGEDEHS.

    Family and domain databases

    Gene3Di3.20.20.440. 1 hit.
    3.40.50.280. 1 hit.
    InterProiIPR016176. Cbl-dep_enz_cat.
    IPR006158. Cobalamin-bd.
    IPR028991. KamE_N.
    IPR015130. Lys-AminoMut_A.
    [Graphical view]
    PfamiPF02310. B12-binding. 1 hit.
    PF09043. Lys-AminoMut_A. 1 hit.
    PF16554. OAM_dimer. 1 hit.
    [Graphical view]
    SUPFAMiSSF51703. SSF51703. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEiPS51332. B12_BINDING. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    E3PY95-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEKDLQLRVN EKLDVENILK DLDKYTPKRR GWTWRQPAEN LQMGPFIYKD
    60 70 80 90 100
    ASTPLENSVA LPSAKYFGDI DPQPLPVITT EIASGRFEDD IRRMRMAAWH
    110 120 130 140 150
    GADHIMVIRT AGQSHYDGLI EGTPQGIGGV PITRKQVRAQ RKALDLIEEE
    160 170 180 190 200
    VGRPINYHSY VSGVAGPDIA VMFAEEGVNG AHQDPQYNVL YRNINMIRSF
    210 220 230 240 250
    IDACESKTIM AWADMAQIDG AHNANATARE AWKVMPELMV QHALNSIFSL
    260 270 280 290 300
    KVGMKKSNIC LSTVPPTAPP APSMYLDLPY AVALREMFEG YRMRAQMNTK
    310 320 330 340 350
    YMEASTREAT VTHVLNLLIS KLTRADIQST ITPDEGRNVP WHIYNIEACD
    360 370 380 390 400
    TAKQALIGMD GLMDMVQLKR EGVLGDTVRE LKERAVLFME EIIEAGGYFN
    410 420 430 440 450
    AVEQGFFVDS GYYPERNGDG IARQINGGIG AGTVFERDED YMAPVTAHFG
    460 470 480 490 500
    YNNVKQYDEA LVSEPSKLID GCTLEVPEKI VYIDELDEND NVNVRMEETK
    510 520 530 540 550
    EFRHSSMIKP EVEWQADGTV LLTMFLPTSK RVAEFAAIEF AKKMNLEEVE
    560 570 580 590 600
    VINREVMQEA EGTRIELKGR VPFSIDINSL VIPPEPEILS EDEIREDIEK
    610 620 630 640 650
    TPLKIVAATV GEDEHSVGLR EVIDIKHGGI EKYGVEVHYL GTSVPVEKLV
    660 670 680 690 700
    DAAIELKADA ILASTIISHD DIHYKNMKRI HELAVEKGIR DKIMIGCGGT
    710 720 730 740
    QVTPEVAVKQ GVDAGFGRGS KGIHVATFLV KKRREMREGK
    Length:740
    Mass (Da):82,765
    Last modified:January 11, 2011 - v1
    Checksum:iA12B500F690213A9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti25 – 251Y → T AA sequence (PubMed:11577113).Curated
    Sequence conflicti220 – 2201G → GIDG in AAK72502 (PubMed:11577113).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY038595 Genomic DNA. Translation: AAK72502.1.
    FP565809 Genomic DNA. Translation: CBH21410.1.

    Genome annotation databases

    EnsemblBacteriaiCBH21410; CBH21410; CLOST_1290.
    KEGGicst:CLOST_1290.
    PATRICi42273211. VBICloSti32817_1277.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY038595 Genomic DNA. Translation: AAK72502.1.
    FP565809 Genomic DNA. Translation: CBH21410.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3KOWX-ray2.90A/B/C/D1-740[»]
    3KOXX-ray2.40A/B/C/D1-740[»]
    3KOYX-ray2.80A/B/C/D1-740[»]
    3KOZX-ray2.80A/B/C/D1-740[»]
    3KP0X-ray2.80A/B/C/D1-740[»]
    3KP1X-ray2.01A/B/C/D1-740[»]
    ProteinModelPortaliE3PY95.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi499177.CLOST_1290.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCBH21410; CBH21410; CLOST_1290.
    KEGGicst:CLOST_1290.
    PATRICi42273211. VBICloSti32817_1277.

    Phylogenomic databases

    eggNOGiENOG4105EQ5. Bacteria.
    ENOG410XSK3. LUCA.
    HOGENOMiHOG000292273.
    KOiK17898.
    OMAiVGEDEHS.

    Enzyme and pathway databases

    BioCyciCSTI499177:GJE9-1338-MONOMER.
    BRENDAi5.4.3.5. 13741.

    Family and domain databases

    Gene3Di3.20.20.440. 1 hit.
    3.40.50.280. 1 hit.
    InterProiIPR016176. Cbl-dep_enz_cat.
    IPR006158. Cobalamin-bd.
    IPR028991. KamE_N.
    IPR015130. Lys-AminoMut_A.
    [Graphical view]
    PfamiPF02310. B12-binding. 1 hit.
    PF09043. Lys-AminoMut_A. 1 hit.
    PF16554. OAM_dimer. 1 hit.
    [Graphical view]
    SUPFAMiSSF51703. SSF51703. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEiPS51332. B12_BINDING. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-ornithine aminomutase from Clostridium sticklandii."
      Chen H.P., Wu S.H., Lin Y.L., Chen C.M., Tsay S.S.
      J. Biol. Chem. 276:44744-44750(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-26, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF HIS-615.
      Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 106541 Publication.
    2. "Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence."
      Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R., Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M., Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.
      BMC Genomics 11:555-555(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654.
    3. "Purification and properties of a pyridoxal phosphate and coenzyme B 12 dependent D-ornithine 5,4-aminomutase."
      Somack R., Costilow R.N.
      Biochemistry 12:2597-2604(1973) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 106541 Publication.
    4. "Amino mutases."
      Baker J.J., Stadtman T.C.
      (In) Dolphin D. (eds.); B12, pp.2:203-231, Wiley Interscience, New York (1982)
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    5. "Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase."
      Wolthers K.R., Levy C., Scrutton N.S., Leys D.
      J. Biol. Chem. 285:13942-13950(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.01 ANGSTROMS) IN COMPLEXES WITH ORAS SUBUNIT; D-ORNITHINE; PYRIDOXAL PHOSPHATE; 5'-DEOXYADENOSYLCOBALAMIN AND 2,4-DIAMINOBUTYRATE, COFACTOR, SUBUNIT, REACTION MECHANISM.
      Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 106541 Publication.

    Entry informationi

    Entry nameiOAME_CLOSD
    AccessioniPrimary (citable) accession number: E3PY95
    Secondary accession number(s): Q8VPJ5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2013
    Last sequence update: January 11, 2011
    Last modified: July 6, 2016
    This is version 27 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, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.