LYS3O_CATAD
ID LYS3O_CATAD Reviewed; 358 AA.
AC C7QJ42;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 1.
DT 03-AUG-2022, entry version 60.
DE RecName: Full=L-lysine 3-hydroxylase {ECO:0000305|Ref.2};
DE EC=1.14.11.- {ECO:0000269|Ref.2};
DE AltName: Full=Alpha-ketoglutarate-dependent dioxygenase {ECO:0000303|Ref.2};
DE AltName: Full=KDO1 {ECO:0000303|Ref.2};
DE AltName: Full=L-lysine hydroxylase {ECO:0000303|Ref.2};
GN OrderedLocusNames=Caci_0231 {ECO:0000312|EMBL:ACU69184.1};
OS Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL
OS B-24433 / ID139908).
OC Bacteria; Actinobacteria; Catenulisporales; Catenulisporaceae;
OC Catenulispora.
OX NCBI_TaxID=479433;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908;
RX PubMed=21304647; DOI=10.4056/sigs.17259;
RA Copeland A., Lapidus A., Glavina Del Rio T., Nolan M., Lucas S., Chen F.,
RA Tice H., Cheng J.F., Bruce D., Goodwin L., Pitluck S., Mikhailova N.,
RA Pati A., Ivanova N., Mavromatis K., Chen A., Palaniappan K., Chain P.,
RA Land M., Hauser L., Chang Y.J., Jeffries C.D., Chertkov O., Brettin T.,
RA Detter J.C., Han C., Ali Z., Tindall B.J., Goker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Catenulispora acidiphila type strain (ID
RT 139908).";
RL Stand. Genomic Sci. 1:119-125(2009).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOTECHNOLOGY.
RX DOI=10.1002/cctc.201402498;
RA Baud D., Saaidi P.-L., Monfleur A., Harari M., Cuccaro J., Fossey A.,
RA Besnard M., Debard A., Mariage A., Pellouin V., Petit J.-L., Salanoubat M.,
RA Weissenbach J., de Berardinis V., Zaparucha A.;
RT "Synthesis of mono- and dihydroxylated amino acids with new alpha-
RT ketoglutarate-dependent dioxygenases: biocatalytic oxidation of C-H
RT bonds.";
RL ChemCatChem 6:3012-3017(2014).
CC -!- FUNCTION: Alpha-ketoglutarate-dependent dioxygenase that in vitro
CC catalyzes the regio- and stereoselective hydroxylation of L-lysine,
CC leading to (3S)-3-hydroxy-L-lysine. Can also use (5R)-5-hydroxy-L-
CC lysine as substrate, but neither D-lysine nor L-ornithine.
CC {ECO:0000269|Ref.2}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + L-lysine + O2 = (3S)-3-hydroxy-L-lysine + CO2
CC + succinate; Xref=Rhea:RHEA:40747, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:77409; Evidence={ECO:0000269|Ref.2};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q9Z4Z5};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9Z4Z5};
CC -!- BIOTECHNOLOGY: Being totally regio- and stereoselective, this enzyme is
CC of interest for biocatalytic purposes to produce chiral scaffolds that
CC are of synthetic value in the preparation of more complex
CC functionalized chiral molecules such as natural products and analogs.
CC {ECO:0000305|Ref.2}.
CC -!- SIMILARITY: Belongs to the clavaminate synthase family. {ECO:0000305}.
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DR EMBL; CP001700; ACU69184.1; -; Genomic_DNA.
DR RefSeq; WP_012784479.1; NC_013131.1.
DR PDB; 6F2A; X-ray; 2.00 A; A/B/C/D=1-358.
DR PDB; 6F2B; X-ray; 2.00 A; A/B/C/D=1-358.
DR PDB; 6F2E; X-ray; 1.90 A; A/B/C/D=1-358.
DR PDB; 6F6J; X-ray; 2.00 A; A/B/C/D=1-358.
DR PDBsum; 6F2A; -.
DR PDBsum; 6F2B; -.
DR PDBsum; 6F2E; -.
DR PDBsum; 6F6J; -.
DR AlphaFoldDB; C7QJ42; -.
DR SMR; C7QJ42; -.
DR STRING; 479433.Caci_0231; -.
DR EnsemblBacteria; ACU69184; ACU69184; Caci_0231.
DR KEGG; cai:Caci_0231; -.
DR eggNOG; COG2175; Bacteria.
DR HOGENOM; CLU_044078_0_0_11; -.
DR OMA; ELTFHTE; -.
DR OrthoDB; 1742732at2; -.
DR Proteomes; UP000000851; Chromosome.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; IDA:UniProtKB.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR Gene3D; 3.60.130.10; -; 1.
DR InterPro; IPR014503; Clavaminate_syn-like.
DR InterPro; IPR042098; TauD-like_sf.
DR InterPro; IPR003819; TauD/TfdA-like.
DR Pfam; PF02668; TauD; 1.
DR PIRSF; PIRSF019543; Clavaminate_syn; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dioxygenase; Iron; Metal-binding; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..358
FT /note="L-lysine 3-hydroxylase"
FT /id="PRO_0000435692"
FT BINDING 178
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q9Z4Z5"
FT BINDING 180
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q9Z4Z5"
FT BINDING 314
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:Q9Z4Z5"
FT BINDING 328
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q9Z4Z5"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 38..40
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 43..53
FT /evidence="ECO:0007829|PDB:6F2E"
FT TURN 60..62
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 64..74
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 80..91
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 126..138
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 161..164
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 170..173
FT /evidence="ECO:0007829|PDB:6F2B"
FT STRAND 175..178
FT /evidence="ECO:0007829|PDB:6F2E"
FT TURN 180..183
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 189..197
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 203..208
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 209..214
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 218..224
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 229..232
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 248..253
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 255..259
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 262..265
FT /evidence="ECO:0007829|PDB:6F2E"
FT TURN 269..271
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 277..293
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 304..308
FT /evidence="ECO:0007829|PDB:6F2E"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 312..316
FT /evidence="ECO:0007829|PDB:6F2E"
FT STRAND 329..337
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 339..345
FT /evidence="ECO:0007829|PDB:6F2E"
FT HELIX 355..357
FT /evidence="ECO:0007829|PDB:6F2E"
SQ SEQUENCE 358 AA; 39194 MW; 1687DA44FCD2B917 CRC64;
MKNLSAYEVY ESPKTSGESR TEAVSEAAFE SDPEVSAILV LTSSEASTLE RVADLVTAHA
LYAAHDFCAQ AQLAAAELPS RVVARLQEFA WGDMNEGHLL IKGLPQVRSL PPTPTSNVHA
VAATTPMSRY QALINECVGR MIAYEAEGHG HTFQDMVPSA MSAHSQTSLG SAVELELHTE
QAFSPLRPDF VSLACLRGDP RALTYLFSAR QLVATLTTQE IAMLREPMWT TTVDESFLAE
GRTFLLGFER GPIPILSGAD DDPFIVFDQD LMRGISAPAQ ELQQTVIRAY YAERVSHCLA
PGEMLLIDNR RAVHGRSIFA PRFDGADRFL SRSFIVADGS RSRHARSSFG RVVSARFS
