LYSK_THET2
ID LYSK_THET2 Reviewed; 361 AA.
AC Q8VUS5;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=[LysW]-lysine hydrolase {ECO:0000255|HAMAP-Rule:MF_01120, ECO:0000305};
DE EC=3.5.1.130 {ECO:0000255|HAMAP-Rule:MF_01120, ECO:0000305|PubMed:19620981};
GN Name=lysK {ECO:0000255|HAMAP-Rule:MF_01120, ECO:0000303|PubMed:11852094};
GN OrderedLocusNames=TT_C1396;
OS Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=262724;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES,
RP PATHWAY, SUBUNIT, DISRUPTION PHENOTYPE, AND GENE NAME.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=11852094; DOI=10.1016/s0014-5793(02)02290-1;
RA Miyazaki J., Kobashi N., Fujii T., Nishiyama M., Yamane H.;
RT "Characterization of a lysK gene as an argE homolog in Thermus thermophilus
RT HB27.";
RL FEBS Lett. 512:269-274(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=15064768; DOI=10.1038/nbt956;
RA Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H.,
RA Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C.,
RA Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P.,
RA Kramer W., Merkl R., Gottschalk G., Fritz H.-J.;
RT "The genome sequence of the extreme thermophile Thermus thermophilus.";
RL Nat. Biotechnol. 22:547-553(2004).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=19620981; DOI=10.1038/nchembio.198;
RA Horie A., Tomita T., Saiki A., Kono H., Taka H., Mineki R., Fujimura T.,
RA Nishiyama C., Kuzuyama T., Nishiyama M.;
RT "Discovery of proteinaceous N-modification in lysine biosynthesis of
RT Thermus thermophilus.";
RL Nat. Chem. Biol. 5:673-679(2009).
RN [4] {ECO:0007744|PDB:5XOY}
RP X-RAY CRYSTALLOGRAPHY (2.39 ANGSTROMS) OF 2-361.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RA Fujita S., Hasebe F., Cho S.H., Tomita T., Kuzuyama T., Nishiyama M.;
RT "Crystal structure of LysK from Thermus thermophilus.";
RL Submitted (JAN-2015) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the release of L-lysine from [LysW]-gamma-L-lysine
CC (Probable). In vitro, can deacetylate both N(2)-acetyl-L-lysine and
CC N(2)-acetyl-L-ornithine (PubMed:11852094).
CC {ECO:0000269|PubMed:11852094, ECO:0000305|PubMed:19620981}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[amino-group carrier protein]-C-terminal-gamma-(L-lysyl)-L-
CC glutamate + H2O = [amino-group carrier protein]-C-terminal-L-
CC glutamate + L-lysine; Xref=Rhea:RHEA:48684, Rhea:RHEA-COMP:9693,
CC Rhea:RHEA-COMP:9715, ChEBI:CHEBI:15377, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:78525, ChEBI:CHEBI:78526; EC=3.5.1.130;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01120,
CC ECO:0000305|PubMed:19620981};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P23908,
CC ECO:0000255|HAMAP-Rule:MF_01120};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000250|UniProtKB:P23908,
CC ECO:0000255|HAMAP-Rule:MF_01120};
CC Note=Binds 2 Zn(2+) or Co(2+) ions per subunit.
CC {ECO:0000250|UniProtKB:P23908, ECO:0000255|HAMAP-Rule:MF_01120};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.3 mM for N(2)-acetyl-L-lysine {ECO:0000269|PubMed:11852094};
CC KM=0.5 mM for N(2)-acetyl-L-ornithine {ECO:0000269|PubMed:11852094};
CC Note=kcat is 51.8 sec(-1) with N(2)-acetyl-L-lysine. kcat is 28.1
CC sec(-1) with N(2)-acetyl-L-ornithine. {ECO:0000269|PubMed:11852094};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
CC pathway; L-lysine from L-alpha-aminoadipate (Thermus route): step 5/5.
CC {ECO:0000255|HAMAP-Rule:MF_01120, ECO:0000269|PubMed:11852094,
CC ECO:0000269|PubMed:19620981}.
CC -!- SUBUNIT: Homotetramer and homooctamer. {ECO:0000269|PubMed:11852094}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01120,
CC ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Knockout mutant shows significantly slow growth
CC in minimal medium, which could be partially restored by the addition of
CC lysine. Exogenous addition of ornithine has a negligible effect on the
CC growth of the mutant, but growth is much improved by the simultaneous
CC addition of lysine and ornithine. {ECO:0000269|PubMed:11852094}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. LysK subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01120, ECO:0000305}.
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DR EMBL; AB063579; BAB79614.1; -; Genomic_DNA.
DR EMBL; AE017221; AAS81738.1; -; Genomic_DNA.
DR RefSeq; WP_011173778.1; NC_005835.1.
DR PDB; 5XOY; X-ray; 2.39 A; A/B=2-361.
DR PDBsum; 5XOY; -.
DR AlphaFoldDB; Q8VUS5; -.
DR SMR; Q8VUS5; -.
DR STRING; 262724.TT_C1396; -.
DR MEROPS; M20.022; -.
DR EnsemblBacteria; AAS81738; AAS81738; TT_C1396.
DR KEGG; tth:TT_C1396; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_2_0_0; -.
DR OMA; HMDTVPG; -.
DR OrthoDB; 906744at2; -.
DR BioCyc; MetaCyc:MON-6742; -.
DR BRENDA; 3.5.1.130; 2305.
DR SABIO-RK; Q8VUS5; -.
DR UniPathway; UPA00033; UER00039.
DR Proteomes; UP000000592; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016811; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019878; P:lysine biosynthetic process via aminoadipic acid; IEA:UniProtKB-UniRule.
DR HAMAP; MF_01120; LysK; 1.
DR InterPro; IPR010175; LysK.
DR InterPro; IPR002933; Peptidase_M20.
DR Pfam; PF01546; Peptidase_M20; 1.
DR TIGRFAMs; TIGR01902; dapE-lys-deAc; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cobalt; Cytoplasm; Hydrolase;
KW Lysine biosynthesis; Metal-binding; Zinc.
FT CHAIN 1..361
FT /note="[LysW]-lysine hydrolase"
FT /id="PRO_0000185343"
FT ACT_SITE 69
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT ACT_SITE 124
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 67
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 125
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 148
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT BINDING 326
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P44514, ECO:0000255|HAMAP-
FT Rule:MF_01120"
FT HELIX 8..16
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 26..38
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 59..67
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 83..86
FT /evidence="ECO:0007829|PDB:5XOY"
FT TURN 87..92
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 93..104
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 114..123
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 130..135
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 161..170
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 183..202
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 212..221
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 228..237
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 243..252
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 258..266
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 276..287
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 293..299
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 302..306
FT /evidence="ECO:0007829|PDB:5XOY"
FT TURN 307..309
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 314..317
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 322..324
FT /evidence="ECO:0007829|PDB:5XOY"
FT STRAND 331..333
FT /evidence="ECO:0007829|PDB:5XOY"
FT HELIX 334..353
FT /evidence="ECO:0007829|PDB:5XOY"
SQ SEQUENCE 361 AA; 39608 MW; 42D0F442E3FAA2B4 CRC64;
MSKSALDPVE FLKGALEIPS PSGKERLVAE YLAEGMQKLG LKGFVDEADN ARGQVGEGPV
QVVLLGHIDT VPGQIPVRLE GGRLFGRGAV DAKGPFVAMI FAAAGLSEEA RKRLTVHLVG
ATEEEAPSSK GARFVAPRLK PHYAVIGEPS GWEGITLGYK GRLLVKARRE KDHFHSAHHE
PNAAEELISY FVAIKAWAEA MNVGQRPFDQ VQYTLRDFRV HPAELRQVAE MFFDLRLPPR
LPPEEAIRHL TAYAPPTIEL EFFGREVPYQ GPKDTPLTRA FRQAIRKAGG RPVFKLKTGT
SDMNVLAPHW PVPMVAYGPG DSTLDHTPYE HVEVAEFLKG IEVLRGALEA LAQTHAGEKE
G
