LYSX_THET8
ID LYSX_THET8 Reviewed; 280 AA.
AC Q5SH23; Q84BR0;
DT 19-JAN-2010, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Alpha-aminoadipate--LysW ligase LysX;
DE Short=AAA--LysW ligase LysX;
DE EC=6.3.2.43 {ECO:0000269|PubMed:19620981};
GN Name=lysX; OrderedLocusNames=TTHA1907;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN
RP COMPLEX WITH ADP, AND SUBUNIT.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=12963379; DOI=10.1016/s0022-2836(03)00946-x;
RA Sakai H., Vassylyeva M.N., Matsuura T., Sekine S., Gotoh K., Nishiyama M.,
RA Terada T., Shirouzu M., Kuramitsu S., Vassylyev D.G., Yokoyama S.;
RT "Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus
RT thermophilus HB8.";
RL J. Mol. Biol. 332:729-740(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
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]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.
RX PubMed=23434852; DOI=10.1038/nchembio.1200;
RA Ouchi T., Tomita T., Horie A., Yoshida A., Takahashi K., Nishida H.,
RA Lassak K., Taka H., Mineki R., Fujimura T., Kosono S., Nishiyama C.,
RA Masui R., Kuramitsu S., Albers S.V., Kuzuyama T., Nishiyama M.;
RT "Lysine and arginine biosyntheses mediated by a common carrier protein in
RT Sulfolobus.";
RL Nat. Chem. Biol. 9:277-283(2013).
CC -!- FUNCTION: Catalyzes the ATP-dependent formation of a covalent bond
CC between the amino group of alpha-aminoadipate (AAA) and the gamma-
CC carboxyl group of the C-terminal glutamate residue in LysW.
CC {ECO:0000269|PubMed:19620981}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[amino-group carrier protein]-C-terminal-L-glutamate + ATP +
CC L-2-aminoadipate = [amino-group carrier protein]-C-terminal-N-(1,4-
CC dicarboxybutan-1-yl)-L-glutamine + ADP + H(+) + phosphate;
CC Xref=Rhea:RHEA:41940, Rhea:RHEA-COMP:9693, Rhea:RHEA-COMP:9694,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58672, ChEBI:CHEBI:78503, ChEBI:CHEBI:78525,
CC ChEBI:CHEBI:456216; EC=6.3.2.43;
CC Evidence={ECO:0000269|PubMed:19620981};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.1 mM for alpha-aminoadipate {ECO:0000269|PubMed:19620981};
CC KM=2.6 mM for ATP {ECO:0000269|PubMed:19620981};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
CC pathway; L-lysine from L-alpha-aminoadipate (Thermus route): step 1/5.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12963379,
CC ECO:0000269|PubMed:23434852}.
CC -!- SIMILARITY: Belongs to the RimK family. LysX subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB103032; BAC67243.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD71730.1; -; Genomic_DNA.
DR RefSeq; WP_011229004.1; NC_006461.1.
DR RefSeq; YP_145173.1; NC_006461.1.
DR PDB; 1UC8; X-ray; 2.00 A; A/B=1-280.
DR PDB; 1UC9; X-ray; 2.38 A; A/B=1-280.
DR PDB; 3VPD; X-ray; 1.95 A; A/B=1-279.
DR PDBsum; 1UC8; -.
DR PDBsum; 1UC9; -.
DR PDBsum; 3VPD; -.
DR AlphaFoldDB; Q5SH23; -.
DR SMR; Q5SH23; -.
DR DIP; DIP-61749N; -.
DR STRING; 300852.55773289; -.
DR PRIDE; Q5SH23; -.
DR EnsemblBacteria; BAD71730; BAD71730; BAD71730.
DR GeneID; 3167971; -.
DR KEGG; ttj:TTHA1907; -.
DR PATRIC; fig|300852.9.peg.1875; -.
DR eggNOG; COG0189; Bacteria.
DR HOGENOM; CLU_054353_2_1_0; -.
DR OMA; CYMNIAS; -.
DR PhylomeDB; Q5SH23; -.
DR BioCyc; MetaCyc:MON-6728; -.
DR BRENDA; 6.3.2.43; 2305.
DR UniPathway; UPA00033; UER00035.
DR EvolutionaryTrace; Q5SH23; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019878; P:lysine biosynthetic process via aminoadipic acid; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.1490.20; -; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013651; ATP-grasp_RimK-type.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR011870; LysX_arch.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR InterPro; IPR004666; RpS6_RimK/Lys_biosynth_LsyX.
DR Pfam; PF08443; RimK; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR02144; LysX_arch; 1.
DR TIGRFAMs; TIGR00768; rimK_fam; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; ATP-binding; Ligase;
KW Lysine biosynthesis; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..280
FT /note="Alpha-aminoadipate--LysW ligase LysX"
FT /id="PRO_0000391001"
FT DOMAIN 93..276
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT MOTIF 258..259
FT /note="N-[TS] motif that is essential for LysX substrate
FT specificity"
FT BINDING 89
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 133..139
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 169..180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 194
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 202
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 237
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 251
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 11..22
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 59..71
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 80..87
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 89..99
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 112..122
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 124..129
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 145..158
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 161..164
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 175..184
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 187..195
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 208..211
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 216..228
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 232..241
FT /evidence="ECO:0007829|PDB:3VPD"
FT STRAND 244..253
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 259..263
FT /evidence="ECO:0007829|PDB:3VPD"
FT HELIX 267..277
FT /evidence="ECO:0007829|PDB:3VPD"
SQ SEQUENCE 280 AA; 30718 MW; B168629146AF1344 CRC64;
MLAILYDRIR PDERMLFERA EALGLPYKKV YVPALPMVLG ERPKELEGVT VALERCVSQS
RGLAAARYLT ALGIPVVNRP EVIEACGDKW ATSVALAKAG LPQPKTALAT DREEALRLME
AFGYPVVLKP VIGSWGRLLA KVTDRAAAEA LLEHKEVLGG FQHQLFYIQE YVEKPGRDIR
VFVVGERAIA AIYRRSAHWI TNTARGGQAE NCPLTEEVAR LSVKAAEAVG GGVVAVDLFE
SERGLLVNEV NHTMEFKNSV HTTGVDIPGE ILKYAWSLAS
