ID OCD_PSEPK Reviewed; 350 AA.
AC Q88H32;
DT 27-SEP-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 27-MAR-2024, entry version 120.
DE RecName: Full=Ornithine cyclodeaminase {ECO:0000303|PubMed:15103146};
DE Short=OCD {ECO:0000303|PubMed:15103146};
DE EC=4.3.1.12 {ECO:0000269|PubMed:23806148};
GN Name=ocd {ECO:0000303|PubMed:23806148};
GN OrderedLocusNames=PP_3533 {ECO:0000312|EMBL:AAN69134.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2]
RP CRYSTALLIZATION.
RX PubMed=15103146; DOI=10.1107/s0907444904005256;
RA Alam S., Wang S.C., Ruzicka F.J., Frey P.A., Wedekind J.E.;
RT "Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase
RT from Pseudomonas putida.";
RL Acta Crystallogr. D 60:941-944(2004).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOTECHNOLOGY, AND PATHWAY.
RX PubMed=23806148; DOI=10.1186/1475-2859-12-63;
RA Jensen J.V., Wendisch V.F.;
RT "Ornithine cyclodeaminase-based proline production by Corynebacterium
RT glutamicum.";
RL Microb. Cell Fact. 12:63-63(2013).
RN [4] {ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEXES WITH NADH AND
RP L-ORNITHINE, COFACTOR, SUBUNIT, REACTION MECHANISM, AND ACTIVE SITE.
RX PubMed=15518536; DOI=10.1021/bi048207i;
RA Goodman J.L., Wang S., Alam S., Ruzicka F.J., Frey P.A., Wedekind J.E.;
RT "Ornithine cyclodeaminase: structure, mechanism of action, and implications
RT for the mu-crystallin family.";
RL Biochemistry 43:13883-13891(2004).
CC -!- FUNCTION: Catalyzes the conversion of L-ornithine into L-proline with
CC release of ammonia. Is likely involved in the L-ornithine degradation
CC pathway that allows P.putida to utilize this compound as sole carbon
CC and nitrogen source. {ECO:0000269|PubMed:23806148}.
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:23806148};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000305|PubMed:15518536};
CC Note=Binds 1 NAD(+) pers subunit. {ECO:0000269|PubMed:15518536};
CC -!- PATHWAY: Amino-acid biosynthesis; L-proline biosynthesis; L-proline
CC from L-ornithine: step 1/1. {ECO:0000269|PubMed:23806148}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15518536}.
CC -!- BIOTECHNOLOGY: Can be used for biotechnological production of L-proline
CC when heterologously overexpressed in C.glutamicum.
CC {ECO:0000269|PubMed:23806148}.
CC -!- SIMILARITY: Belongs to the ornithine cyclodeaminase/mu-crystallin
CC family. {ECO:0000305}.
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DR EMBL; AE015451; AAN69134.1; -; Genomic_DNA.
DR RefSeq; NP_745670.1; NC_002947.4.
DR RefSeq; WP_010954390.1; NC_002947.4.
DR PDB; 1U7H; X-ray; 1.80 A; A/B=1-350.
DR PDB; 1X7D; X-ray; 1.60 A; A/B=1-350.
DR PDBsum; 1U7H; -.
DR PDBsum; 1X7D; -.
DR AlphaFoldDB; Q88H32; -.
DR SMR; Q88H32; -.
DR STRING; 160488.PP_3533; -.
DR DrugBank; DB03814; 2-(N-morpholino)ethanesulfonic acid.
DR PaxDb; 160488-PP_3533; -.
DR GeneID; 83679759; -.
DR KEGG; ppu:PP_3533; -.
DR PATRIC; fig|160488.4.peg.3757; -.
DR eggNOG; COG2423; Bacteria.
DR HOGENOM; CLU_042088_3_2_6; -.
DR OrthoDB; 9809203at2; -.
DR PhylomeDB; Q88H32; -.
DR BioCyc; PPUT160488:G1G01-3769-MONOMER; -.
DR BRENDA; 4.3.1.12; 5092.
DR UniPathway; UPA00098; UER00357.
DR EvolutionaryTrace; Q88H32; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
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; ornithine cyclodeaminase, domain 1; 2.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR003462; ODC_Mu_crystall.
DR InterPro; IPR023401; ODC_N.
DR PANTHER; PTHR13812; KETIMINE REDUCTASE MU-CRYSTALLIN; 1.
DR PANTHER; PTHR13812:SF19; KETIMINE REDUCTASE MU-CRYSTALLIN; 1.
DR Pfam; PF02423; OCD_Mu_crystall; 1.
DR PIRSF; PIRSF001439; CryM; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Lyase; NAD; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..350
FT /note="Ornithine cyclodeaminase"
FT /id="PRO_0000441722"
FT ACT_SITE 228
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 45
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 69
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 84
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 112
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 139..140
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 161
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 202
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 225..228
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 228
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 293
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT BINDING 294
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1X7D"
FT BINDING 331
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:15518536,
FT ECO:0007744|PDB:1U7H, ECO:0007744|PDB:1X7D"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 7..17
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 19..35
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 54..61
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 63..73
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 75..80
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 84..93
FT /evidence="ECO:0007829|PDB:1X7D"
FT TURN 94..96
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 106..124
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 156..160
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 164..174
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 188..192
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 205..211
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 221..224
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 232..235
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 237..241
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 250..256
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 258..261
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 271..275
FT /evidence="ECO:0007829|PDB:1X7D"
FT STRAND 289..292
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 297..312
FT /evidence="ECO:0007829|PDB:1X7D"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:1X7D"
FT HELIX 334..337
FT /evidence="ECO:0007829|PDB:1X7D"
FT TURN 339..341
FT /evidence="ECO:0007829|PDB:1U7H"
SQ SEQUENCE 350 AA; 38425 MW; 29323AD3D54F847B CRC64;
MTYFIDVPTM SDLVHDIGVA PFIGELAAAL RDDFKRWQAF DKSARVASHS EVGVIELMPV
ADKSRYAFKY VNGHPANTAR NLHTVMAFGV LADVDSGYPV LLSELTIATA LRTAATSLMA
AQALARPNAR KMALIGNGAQ SEFQALAFHK HLGIEEIVAY DTDPLATAKL IANLKEYSGL
TIRRASSVAE AVKGVDIITT VTADKAYATI ITPDMLEPGM HLNAVGGDCP GKTELHADVL
RNARVFVEYE PQTRIEGEIQ QLPADFPVVD LWRVLRGETE GRQSDSQVTV FDSVGFALED
YTVLRYVLQQ AEKRGMGTKI DLVPWVEDDP KDLFSHTRGR AGKRRIRRVA
//
