OCD_AGRFC
ID OCD_AGRFC Reviewed; 354 AA.
AC P09773;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 27-MAR-2002, sequence version 2.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Ornithine cyclodeaminase {ECO:0000303|PubMed:3281832};
DE Short=OCD {ECO:0000303|PubMed:3281832};
DE EC=4.3.1.12 {ECO:0000269|PubMed:3281832};
GN Name=ocd {ECO:0000303|PubMed:3281832}; OrderedLocusNames=Atu6016;
GN ORFNames=AGR_pTi_54;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OG Plasmid pTiC58.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, INDUCTION, AND PATHWAY.
RX PubMed=3281832; DOI=10.1111/j.1432-1033.1988.tb13975.x;
RA Sans N., Schindler U., Schroeder J.;
RT "Ornithine cyclodeaminase from Ti plasmid C58: DNA sequence, enzyme
RT properties and regulation of activity by arginine.";
RL Eur. J. Biochem. 173:123-130(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8045881; DOI=10.1128/jb.176.15.4511-4517.1994;
RA Zanker H., Lurz G., Langridge U., Langridge P., Kreusch D., Schroeder J.;
RT "Octopine and nopaline oxidases from Ti plasmids of Agrobacterium
RT tumefaciens: molecular analysis, relationship, and functional
RT characterization.";
RL J. Bacteriol. 176:4511-4517(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
CC -!- FUNCTION: Catalyzes the conversion of L-ornithine into L-proline with
CC release of ammonia. Is involved in the utilization of nopaline, a
CC catabolic pathway that proceeds through L-arginine and L-ornithine to
CC L-proline. Nopaline is a predominant opine in plant cells transformed
CC with Ti plasmid pTiC58. {ECO:0000269|PubMed:3281832}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-ornithine = L-proline + NH4(+); Xref=Rhea:RHEA:24368,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:46911, ChEBI:CHEBI:60039; EC=4.3.1.12;
CC Evidence={ECO:0000269|PubMed:3281832};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000269|PubMed:3281832};
CC -!- ACTIVITY REGULATION: Is subject to substrate inhibition. Is regulated
CC by L-arginine, which stimulates enzymatic activity at 0.1-1 mM while
CC inhibits activity at higher concentrations, and has pronounced effects
CC on the optima for pH and temperature and on the Km for L-ornithine. Is
CC not inhibited by L-proline. {ECO:0000269|PubMed:3281832}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.7 mM for L-ornithine (in the absence of L-arginine)
CC {ECO:0000269|PubMed:3281832};
CC KM=0.25 mM for L-ornithine (in the presence of 1 mM L-arginine)
CC {ECO:0000269|PubMed:3281832};
CC KM=8 uM for NAD(+) {ECO:0000269|PubMed:3281832};
CC pH dependence:
CC Optimum pH is 8.0-9.5 in the presence of L-arginine, and 8.5-9.0 in
CC the presence of 1 mM L-arginine. {ECO:0000269|PubMed:3281832};
CC Temperature dependence:
CC Optimum temperature is 25-35 degrees Celsius in the presence of L-
CC arginine, and 38-42 degrees Celsius in the presence of 1 mM L-
CC arginine. {ECO:0000269|PubMed:3281832};
CC -!- PATHWAY: Amino-acid biosynthesis; L-proline biosynthesis; L-proline
CC from L-ornithine: step 1/1. {ECO:0000269|PubMed:3281832}.
CC -!- INDUCTION: Is induced by nopaline. {ECO:0000269|PubMed:3281832}.
CC -!- SIMILARITY: Belongs to the ornithine cyclodeaminase/mu-crystallin
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAK90974.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X07435; CAA30316.1; -; Genomic_DNA.
DR EMBL; Z30316; CAA82966.1; -; Genomic_DNA.
DR EMBL; AE007871; AAK90974.1; ALT_INIT; Genomic_DNA.
DR PIR; AF3229; AF3229.
DR PIR; S00402; DUAGO.
DR PIR; S55582; S55582.
DR RefSeq; NP_396533.3; NC_003065.3.
DR RefSeq; WP_010891456.1; NC_003065.3.
DR AlphaFoldDB; P09773; -.
DR SMR; P09773; -.
DR PRIDE; P09773; -.
DR EnsemblBacteria; AAK90974; AAK90974; Atu6016.
DR KEGG; atu:Atu6016; -.
DR PATRIC; fig|176299.10.peg.5223; -.
DR HOGENOM; CLU_042088_3_2_5; -.
DR OMA; EYIRQDY; -.
DR BioCyc; MetaCyc:MON-11553; -.
DR SABIO-RK; P09773; -.
DR UniPathway; UPA00098; UER00357.
DR Proteomes; UP000000813; Plasmid Ti.
DR GO; GO:0008473; F:ornithine cyclodeaminase activity; IEA:UniProtKB-EC.
DR GO; GO:0055129; P:L-proline biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.1780.10; -; 1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR003462; ODC_Mu_crystall.
DR InterPro; IPR023401; ODC_N.
DR PANTHER; PTHR13812; PTHR13812; 1.
DR Pfam; PF02423; OCD_Mu_crystall; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW Lyase; NAD; Plasmid; Reference proteome.
FT CHAIN 1..354
FT /note="Ornithine cyclodeaminase"
FT /id="PRO_0000200669"
FT ACT_SITE 235
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 53
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 77
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 92
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 120
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 120
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 147..148
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 169
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 209
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 232..235
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 235
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 239
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 300
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT BINDING 301
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000250|UniProtKB:Q88H32"
FT CONFLICT 212
FT /note="K -> E (in Ref. 1 and 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 297
FT /note="L -> I (in Ref. 1 and 2)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 354 AA; 38983 MW; 8272024E0BFDBA24 CRC64;
MPALANLNIV PFISVENMMD LAVSTGIENF LVQLAGYIEE DFRRWESFDK IPRIASHSRD
GVIELMPTSD GTLYGFKYVN GHPKNTKSGR QTVTAFGVLS DVDSGYPLLL SEMTILTALR
TAATSAIAAK YLARKDSRTM ALIGNGAQSE FQALAFKALI GVDRIRLYDI DPEATARCSR
NLQRFGFQIE ACTSAEQAVE GADIITTATA DKHNATILSD NMIGPGVHIN GVGGDCPGKT
EMHRDILLRS DIFVEFPPQT RIEGEIQQLA PDHPVTELWR VMTGQDVGRK SDKQITLFDS
VGFAIEDFSA LRYVRDRVEG SSHSSPLDLL ADPDEPRDLF GMLLRRQAFR RLGG
