Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei81Substrate1 Publication1
    Binding sitei160Substrate1
    Binding sitei182Substrate1 Publication1
    Metal bindingi615Cobalt (adenosylcobalamin axial ligand); via tele nitrogen1 Publication1
    Binding sitei700Adenosylcobalamin1
    Binding sitei720Adenosylcobalamin1

    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 lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeAcetoanaerobium
    Proteomesi
    • UP000007041 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi615H → G: Loss of corrinoid-binding ability. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004218051 – 740D-ornithine 4,5-aminomutase subunit betaAdd BLAST740

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei626N6-(pyridoxal phosphate)lysine1 Publication1

    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

    1740
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi15 – 18Combined sources4
    Turni19 – 21Combined sources3
    Helixi22 – 24Combined sources3
    Beta strandi41 – 43Combined sources3
    Beta strandi46 – 52Combined sources7
    Helixi62 – 67Combined sources6
    Beta strandi73 – 81Combined sources9
    Helixi87 – 99Combined sources13
    Beta strandi104 – 106Combined sources3
    Helixi113 – 115Combined sources3
    Beta strandi127 – 130Combined sources4
    Helixi134 – 151Combined sources18
    Beta strandi156 – 160Combined sources5
    Helixi166 – 176Combined sources11
    Beta strandi180 – 182Combined sources3
    Helixi185 – 192Combined sources8
    Helixi196 – 212Combined sources17
    Beta strandi216 – 218Combined sources3
    Helixi222 – 227Combined sources6
    Beta strandi228 – 230Combined sources3
    Helixi231 – 233Combined sources3
    Helixi235 – 252Combined sources18
    Helixi256 – 258Combined sources3
    Beta strandi259 – 263Combined sources5
    Helixi273 – 287Combined sources15
    Turni288 – 290Combined sources3
    Beta strandi291 – 295Combined sources5
    Helixi306 – 322Combined sources17
    Beta strandi326 – 328Combined sources3
    Turni333 – 337Combined sources5
    Helixi342 – 358Combined sources17
    Turni359 – 361Combined sources3
    Helixi362 – 364Combined sources3
    Beta strandi366 – 368Combined sources3
    Beta strandi370 – 372Combined sources3
    Helixi373 – 394Combined sources22
    Helixi398 – 403Combined sources6
    Turni430 – 432Combined sources3
    Beta strandi445 – 447Combined sources3
    Helixi455 – 458Combined sources4
    Helixi459 – 461Combined sources3
    Helixi465 – 469Combined sources5
    Turni473 – 475Combined sources3
    Helixi477 – 479Combined sources3
    Beta strandi488 – 491Combined sources4
    Helixi492 – 498Combined sources7
    Helixi499 – 502Combined sources4
    Beta strandi512 – 514Combined sources3
    Beta strandi519 – 528Combined sources10
    Helixi530 – 543Combined sources14
    Beta strandi547 – 558Combined sources12
    Turni559 – 561Combined sources3
    Beta strandi562 – 570Combined sources9
    Helixi577 – 579Combined sources3
    Helixi591 – 600Combined sources10
    Beta strandi604 – 610Combined sources7
    Helixi617 – 621Combined sources5
    Turni625 – 628Combined sources4
    Helixi630 – 633Combined sources4
    Beta strandi636 – 639Combined sources4
    Beta strandi642 – 644Combined sources3
    Helixi646 – 655Combined sources10
    Beta strandi659 – 664Combined sources6
    Helixi669 – 671Combined sources3
    Helixi672 – 686Combined sources15
    Turni690 – 692Combined sources3
    Beta strandi693 – 698Combined sources6
    Helixi704 – 708Combined sources5
    Turni709 – 711Combined sources3
    Beta strandi713 – 716Combined sources4
    Helixi722 – 736Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiE3PY95.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini602 – 739B12-bindingPROSITE-ProRule annotationAdd BLAST138

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni294 – 296Substrate binding3
    Regioni614 – 616Adenosylcobalamin binding1 Publication3
    Regioni664 – 669Adenosylcobalamin binding1 Publication6

    Sequence similaritiesi

    Contains 1 B12-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105EQ5. Bacteria.
    ENOG410XSK3. LUCA.
    HOGENOMiHOG000292273.
    KOiK17898.
    OMAiVGEDEHS.
    OrthoDBiPOG091H0U91.

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti25Y → T AA sequence (PubMed:11577113).Curated1
    Sequence conflicti220G → GIDG in AAK72502 (PubMed:11577113).Curated1

    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
    PDB 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.
    SMRiE3PY95.
    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.
    OrthoDBiPOG091H0U91.

    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...

    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: November 30, 2016
    This is version 30 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.