OAME_ACESD
ID OAME_ACESD Reviewed; 740 AA.
AC E3PY95; Q8VPJ5;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 11-JAN-2011, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=D-ornithine 4,5-aminomutase subunit beta;
DE EC=5.4.3.5 {ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
DE AltName: Full=D-ornithine aminomutase E component {ECO:0000303|PubMed:11577113};
DE Short=OAM-E;
GN Name=oraE; OrderedLocusNames=CLOST_1290;
OS Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG
OS 9281 / NCIMB 10654 / HF) (Clostridium sticklandii).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Acetoanaerobium.
OX NCBI_TaxID=499177;
RN [1] {ECO:0000305, ECO:0000312|EMBL:AAK72502.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-26, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP MUTAGENESIS OF HIS-615.
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF
RC {ECO:0000269|PubMed:11577113};
RX PubMed=11577113; DOI=10.1074/jbc.m108365200;
RA Chen H.P., Wu S.H., Lin Y.L., Chen C.M., Tsay S.S.;
RT "Cloning, sequencing, heterologous expression, purification, and
RT characterization of adenosylcobalamin-dependent D-ornithine aminomutase
RT from Clostridium sticklandii.";
RL J. Biol. Chem. 276:44744-44750(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF;
RX PubMed=20937090; DOI=10.1186/1471-2164-11-555;
RA Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R.,
RA Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M.,
RA Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.;
RT "Clostridium sticklandii, a specialist in amino acid degradation:revisiting
RT its metabolism through its genome sequence.";
RL BMC Genomics 11:555-555(2010).
RN [3] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, SUBSTRATE
RP SPECIFICITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF
RC {ECO:0000269|PubMed:4711468};
RX PubMed=4711468; DOI=10.1021/bi00738a008;
RA Somack R., Costilow R.N.;
RT "Purification and properties of a pyridoxal phosphate and coenzyme B 12
RT dependent D-ornithine 5,4-aminomutase.";
RL Biochemistry 12:2597-2604(1973).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, SUBSTRATE
RP SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RA Baker J.J., Stadtman T.C.;
RT "Amino mutases.";
RL (In) Dolphin D. (eds.);
RL B12, pp.2:203-231, Wiley Interscience, New York (1982).
RN [5] {ECO:0000305, ECO:0000312|PDB:3KP0}
RP X-RAY CRYSTALLOGRAPHY (2.01 ANGSTROMS) IN COMPLEXES WITH ORAS SUBUNIT;
RP D-ORNITHINE; PYRIDOXAL PHOSPHATE; 5'-DEOXYADENOSYLCOBALAMIN AND
RP 2,4-DIAMINOBUTYRATE, COFACTOR, SUBUNIT, AND REACTION MECHANISM.
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF
RC {ECO:0000269|PubMed:20106986};
RX PubMed=20106986; DOI=10.1074/jbc.m109.068908;
RA Wolthers K.R., Levy C., Scrutton N.S., Leys D.;
RT "Large-scale domain dynamics and adenosylcobalamin reorientation
RT orchestrate radical catalysis in ornithine 4,5-aminomutase.";
RL J. Biol. Chem. 285:13942-13950(2010).
CC -!- FUNCTION: Component of a complex that catalyzes the reversible
CC migration of the omega amino group of D-ornithine to C-4 to form
CC (2R,4S)-2,4-diaminopentanoic acid. OraE may be the catalytic subunit.
CC Active only on D-ornithine and 2,4-diaminopentanoic acid but not active
CC on L-ornithine, L-beta-lysine, L-alpha-lysine or D-alpha-lysine.
CC {ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:4711468,
CC ECO:0000269|Ref.4}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ornithine = (2R,4S)-2,4-diaminopentanoate;
CC Xref=Rhea:RHEA:14893, ChEBI:CHEBI:57668, ChEBI:CHEBI:58697;
CC EC=5.4.3.5; Evidence={ECO:0000269|PubMed:11577113,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:20106986,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:20106986,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC -!- ACTIVITY REGULATION: Increased activity in the presence of
CC dithiothreitol (DTT) in vitro. Inhibited by 1 mM potassium phosphate
CC and potassium chloride. Inhibited by L-alpha-ornithine, D,L-alpha-
CC lysine, L-beta-lysine (50%-60%), L-alpha-lysine (26%) and by delta-
CC amino-n-valeric acid to a lesser extent. Significant decrease in
CC activity is observed in the presence of 0.2 mM p-chloromercuribenzoate,
CC N-ethylmaleimide and also by 2 mM iodoacetate to a lesser extent but
CC not inhibited by arsenite. {ECO:0000269|PubMed:4711468,
CC ECO:0000269|Ref.4}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=44.5 uM for D-ornithine {ECO:0000269|PubMed:11577113,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC KM=0.43 uM for adenosylcobalamin {ECO:0000269|PubMed:11577113,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC KM=1.5 uM for pyridoxal phosphate {ECO:0000269|PubMed:11577113,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC Note=kcat is 6.3 sec(-1). Values are measured for recombinant S and E
CC components expressed together in E.coli to overcome the presence of
CC corrinoids in native system.;
CC pH dependence:
CC Optimum pH is 9.0 or between 8.5-8.7 (with Tris-HCl buffer). Half-
CC maximal activity is observed at pH 7.4 and 9.7.
CC {ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:4711468,
CC ECO:0000269|Ref.4};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius for native enzyme. Displays
CC half-maximal activity at 23 degrees Celsius and 49 degrees Celsius.
CC Rapidly inactivated at temperatures above 45 degrees Celsius. Loses
CC more than 35% and 30% of its activity when stored at -20 degrees
CC Celsius for 1 month and at 4 degrees Celsius for 48 hours,
CC respectively. {ECO:0000269|PubMed:11577113,
CC ECO:0000269|PubMed:4711468, ECO:0000269|Ref.4};
CC -!- SUBUNIT: Heterotetramer of 2 alpha (OraS) and 2 beta (OraE) subunits.
CC {ECO:0000269|PubMed:11577113, ECO:0000269|PubMed:20106986,
CC ECO:0000269|Ref.4}.
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DR EMBL; AY038595; AAK72502.1; -; Genomic_DNA.
DR EMBL; FP565809; CBH21410.1; -; Genomic_DNA.
DR PDB; 3KOW; X-ray; 2.90 A; A/B/C/D=1-740.
DR PDB; 3KOX; X-ray; 2.40 A; A/B/C/D=1-740.
DR PDB; 3KOY; X-ray; 2.80 A; A/B/C/D=1-740.
DR PDB; 3KOZ; X-ray; 2.80 A; A/B/C/D=1-740.
DR PDB; 3KP0; X-ray; 2.80 A; A/B/C/D=1-740.
DR PDB; 3KP1; X-ray; 2.01 A; A/B/C/D=1-740.
DR PDBsum; 3KOW; -.
DR PDBsum; 3KOX; -.
DR PDBsum; 3KOY; -.
DR PDBsum; 3KOZ; -.
DR PDBsum; 3KP0; -.
DR PDBsum; 3KP1; -.
DR AlphaFoldDB; E3PY95; -.
DR SMR; E3PY95; -.
DR STRING; 1511.CLOST_1290; -.
DR EnsemblBacteria; CBH21410; CBH21410; CLOST_1290.
DR KEGG; cst:CLOST_1290; -.
DR eggNOG; COG5012; Bacteria.
DR HOGENOM; CLU_027795_0_0_9; -.
DR OMA; AWKVMPE; -.
DR BioCyc; MetaCyc:MON-12493; -.
DR BRENDA; 5.4.3.5; 1522.
DR Proteomes; UP000007041; Chromosome.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0047831; F:D-ornithine 4,5-aminomutase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR Gene3D; 3.20.20.440; -; 1.
DR Gene3D; 3.30.30.60; -; 1.
DR InterPro; IPR016176; Cbl-dep_enz_cat.
DR InterPro; IPR006158; Cobalamin-bd.
DR InterPro; IPR036724; Cobalamin-bd_sf.
DR InterPro; IPR028991; KamE_N.
DR InterPro; IPR036843; KamE_N_sf.
DR InterPro; IPR015130; Lys-AminoMut_A.
DR InterPro; IPR037086; Lys-AminoMut_asu_sf.
DR Pfam; PF02310; B12-binding; 1.
DR Pfam; PF09043; Lys-AminoMut_A; 1.
DR Pfam; PF16554; OAM_dimer; 1.
DR SUPFAM; SSF51703; SSF51703; 1.
DR SUPFAM; SSF52242; SSF52242; 1.
DR PROSITE; PS51332; B12_BINDING; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalamin; Cobalt; Direct protein sequencing; Isomerase;
KW Metal-binding; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..740
FT /note="D-ornithine 4,5-aminomutase subunit beta"
FT /id="PRO_0000421805"
FT DOMAIN 602..739
FT /note="B12-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00666"
FT BINDING 81
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20106986"
FT BINDING 160
FT /ligand="substrate"
FT BINDING 182
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20106986"
FT BINDING 294..296
FT /ligand="substrate"
FT BINDING 614..616
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT /evidence="ECO:0000269|PubMed:20106986"
FT BINDING 615
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT /ligand_part="Co"
FT /ligand_part_id="ChEBI:CHEBI:27638"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:20106986"
FT BINDING 664..669
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT /evidence="ECO:0000269|PubMed:20106986"
FT BINDING 700
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT BINDING 720
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT MOD_RES 626
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:20106986"
FT MUTAGEN 615
FT /note="H->G: Loss of corrinoid-binding ability."
FT /evidence="ECO:0000269|PubMed:11577113"
FT CONFLICT 25
FT /note="Y -> T (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 220
FT /note="G -> GIDG (in Ref. 1; AAK72502)"
FT /evidence="ECO:0000305"
FT HELIX 15..18
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 62..67
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 73..81
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 87..99
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 127..130
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 134..151
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 156..160
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 166..176
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 185..192
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 196..212
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 216..218
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 222..227
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:3KOW"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 235..252
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 273..287
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 288..290
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 291..295
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 306..322
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 326..328
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 333..337
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 342..358
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 362..364
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 370..372
FT /evidence="ECO:0007829|PDB:3KOW"
FT HELIX 373..394
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 398..403
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 430..432
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 445..447
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 455..458
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 459..461
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 465..469
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 473..475
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 477..479
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 488..491
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 492..498
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 499..502
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 512..514
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 519..528
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 530..543
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 547..558
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 559..561
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 562..570
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 577..579
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 591..600
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 604..610
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 617..621
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 625..628
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 630..633
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 636..639
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 642..644
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 646..655
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 659..664
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 669..671
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 672..686
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 690..692
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 693..698
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 704..708
FT /evidence="ECO:0007829|PDB:3KP1"
FT TURN 709..711
FT /evidence="ECO:0007829|PDB:3KP1"
FT STRAND 713..716
FT /evidence="ECO:0007829|PDB:3KP1"
FT HELIX 722..736
FT /evidence="ECO:0007829|PDB:3KP1"
SQ SEQUENCE 740 AA; 82765 MW; A12B500F690213A9 CRC64;
MEKDLQLRVN EKLDVENILK DLDKYTPKRR GWTWRQPAEN LQMGPFIYKD ASTPLENSVA
LPSAKYFGDI DPQPLPVITT EIASGRFEDD IRRMRMAAWH GADHIMVIRT AGQSHYDGLI
EGTPQGIGGV PITRKQVRAQ RKALDLIEEE VGRPINYHSY VSGVAGPDIA VMFAEEGVNG
AHQDPQYNVL YRNINMIRSF IDACESKTIM AWADMAQIDG AHNANATARE AWKVMPELMV
QHALNSIFSL KVGMKKSNIC LSTVPPTAPP APSMYLDLPY AVALREMFEG YRMRAQMNTK
YMEASTREAT VTHVLNLLIS KLTRADIQST ITPDEGRNVP WHIYNIEACD TAKQALIGMD
GLMDMVQLKR EGVLGDTVRE LKERAVLFME EIIEAGGYFN AVEQGFFVDS GYYPERNGDG
IARQINGGIG AGTVFERDED YMAPVTAHFG YNNVKQYDEA LVSEPSKLID GCTLEVPEKI
VYIDELDEND NVNVRMEETK EFRHSSMIKP EVEWQADGTV LLTMFLPTSK RVAEFAAIEF
AKKMNLEEVE VINREVMQEA EGTRIELKGR VPFSIDINSL VIPPEPEILS EDEIREDIEK
TPLKIVAATV GEDEHSVGLR EVIDIKHGGI EKYGVEVHYL GTSVPVEKLV DAAIELKADA
ILASTIISHD DIHYKNMKRI HELAVEKGIR DKIMIGCGGT QVTPEVAVKQ GVDAGFGRGS
KGIHVATFLV KKRREMREGK
