SERK_THEKO
ID SERK_THEKO Reviewed; 242 AA.
AC Q5JD03;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=L-serine kinase SerK {ECO:0000305};
DE EC=2.7.1.226 {ECO:0000269|PubMed:27857065, ECO:0000269|PubMed:28358477};
GN Name=serK {ECO:0000303|PubMed:28358477};
GN OrderedLocusNames=TK0378 {ECO:0000312|EMBL:BAD84567.1};
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=27857065; DOI=10.1038/ncomms13446;
RA Makino Y., Sato T., Kawamura H., Hachisuka S.I., Takeno R., Imanaka T.,
RA Atomi H.;
RT "An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis
RT and serine metabolism.";
RL Nat. Commun. 7:13446-13446(2016).
RN [3] {ECO:0000312|PDB:5X0G, ECO:0000312|PDB:5X0K, ECO:0007744|PDB:5X0B, ECO:0007744|PDB:5X0E, ECO:0007744|PDB:5X0F, ECO:0007744|PDB:5X0J}
RP X-RAY CRYSTALLOGRAPHY (1.43 ANGSTROMS) OF WILD-TYPE AND MUTANTS ALA-30 AND
RP GLN-30 IN COMPLEXES WITH ADP; AMP AND PHOSPHOSERINE, FUNCTION, CATALYTIC
RP ACTIVITY, MUTAGENESIS OF GLU-4; GLU-30; GLU-36 AND ASP-69, AND ACTIVE SITE.
RX PubMed=28358477; DOI=10.1021/acschembio.7b00064;
RA Nagata R., Fujihashi M., Kawamura H., Sato T., Fujita T., Atomi H.,
RA Miki K.;
RT "Structural study on the reaction mechanism of a free serine kinase
RT involved in cysteine biosynthesis.";
RL ACS Chem. Biol. 12:1514-1523(2017).
CC -!- FUNCTION: Free serine kinase that uses ADP to phosphorylate L-serine to
CC yield O-phospho-L-serine and AMP. {ECO:0000269|PubMed:27857065,
CC ECO:0000269|PubMed:28358477}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ADP + L-serine = AMP + H(+) + O-phospho-L-serine;
CC Xref=Rhea:RHEA:59176, ChEBI:CHEBI:15378, ChEBI:CHEBI:33384,
CC ChEBI:CHEBI:57524, ChEBI:CHEBI:456215, ChEBI:CHEBI:456216;
CC EC=2.7.1.226; Evidence={ECO:0000269|PubMed:27857065,
CC ECO:0000269|PubMed:28358477};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.1 mM for serine {ECO:0000269|PubMed:27857065};
CC KM=2.4 mM for ADP {ECO:0000269|PubMed:27857065};
CC Note=kcat is 218 sec(-1) with serine as substrate. kcat is 204 sec(-
CC 1) with ADP as substrate. {ECO:0000269|PubMed:27857065};
CC -!- PATHWAY: Amino-acid biosynthesis; L-cysteine biosynthesis; L-cysteine
CC from L-serine: step 1/2. {ECO:0000269|PubMed:27857065}.
CC -!- DISRUPTION PHENOTYPE: Disruption of gene does not lead to complete Cys
CC auxotrophy, but mutant displays a growth defect in an amino acid medium
CC depleted of Cys. {ECO:0000269|PubMed:27857065}.
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DR EMBL; AP006878; BAD84567.1; -; Genomic_DNA.
DR RefSeq; WP_011249333.1; NC_006624.1.
DR PDB; 5X0B; X-ray; 1.75 A; A=1-242.
DR PDB; 5X0E; X-ray; 2.00 A; A=1-242.
DR PDB; 5X0F; X-ray; 1.76 A; A=1-242.
DR PDB; 5X0G; X-ray; 1.90 A; A=1-242.
DR PDB; 5X0J; X-ray; 1.43 A; A=1-242.
DR PDB; 5X0K; X-ray; 1.65 A; A=1-242.
DR PDBsum; 5X0B; -.
DR PDBsum; 5X0E; -.
DR PDBsum; 5X0F; -.
DR PDBsum; 5X0G; -.
DR PDBsum; 5X0J; -.
DR PDBsum; 5X0K; -.
DR AlphaFoldDB; Q5JD03; -.
DR SMR; Q5JD03; -.
DR STRING; 69014.TK0378; -.
DR EnsemblBacteria; BAD84567; BAD84567; TK0378.
DR GeneID; 3235225; -.
DR KEGG; tko:TK0378; -.
DR PATRIC; fig|69014.16.peg.375; -.
DR eggNOG; arCOG01875; Archaea.
DR HOGENOM; CLU_1088213_0_0_2; -.
DR InParanoid; Q5JD03; -.
DR OMA; GHHRWAG; -.
DR OrthoDB; 76894at2157; -.
DR PhylomeDB; Q5JD03; -.
DR BioCyc; MetaCyc:MON-20566; -.
DR BRENDA; 2.7.1.226; 5246.
DR UniPathway; UPA00136; UER00199.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0019344; P:cysteine biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1760.10; -; 1.
DR InterPro; IPR040867; DUF5603.
DR InterPro; IPR003115; ParB/Sulfiredoxin_dom.
DR InterPro; IPR036086; ParB/Sulfiredoxin_sf.
DR InterPro; IPR023098; SerK/SbnI_C.
DR Pfam; PF18231; DUF5603; 1.
DR Pfam; PF02195; ParBc; 1.
DR SMART; SM00470; ParB; 1.
DR SUPFAM; SSF110849; SSF110849; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Nucleotide-binding; Reference proteome;
KW Transferase.
FT CHAIN 1..242
FT /note="L-serine kinase SerK"
FT /id="PRO_0000447122"
FT ACT_SITE 30
FT /evidence="ECO:0000305|PubMed:28358477"
FT BINDING 43
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:28358477"
FT BINDING 49..52
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:28358477"
FT BINDING 68..72
FT /ligand="O-phospho-L-serine"
FT /ligand_id="ChEBI:CHEBI:57524"
FT /evidence="ECO:0000269|PubMed:28358477"
FT BINDING 69..73
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:28358477"
FT BINDING 102
FT /ligand="O-phospho-L-serine"
FT /ligand_id="ChEBI:CHEBI:57524"
FT /evidence="ECO:0000269|PubMed:28358477"
FT BINDING 221..225
FT /ligand="O-phospho-L-serine"
FT /ligand_id="ChEBI:CHEBI:57524"
FT /evidence="ECO:0000269|PubMed:28358477"
FT MUTAGEN 4
FT /note="E->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:28358477"
FT MUTAGEN 30
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28358477"
FT MUTAGEN 36
FT /note="E->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:28358477"
FT MUTAGEN 69
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28358477"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:5X0B"
FT STRAND 19..22
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 34..47
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 71..80
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 84..90
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 110..119
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 130..135
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 138..151
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 155..170
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 173..180
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 205..213
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:5X0J"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:5X0J"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:5X0J"
SQ SEQUENCE 242 AA; 27698 MW; 826860F4146091C0 CRC64;
MGVEKVPKYD IPTKKVDYVF IELDKMKPHE QLVQKELEAF IESVTGSGIF WKPMLLAKVP
GEDMYLIVDG HHRWAGLQKL GAKRAPSVIL DYFSDDVKVY TWYPAFKGDL NEVVERLKKE
GLEVIEDPEA EEKAERGEIA FALVGEKSFA IPGGLEEQKK VSKVLDEMSV EGKIELIYYG
LKEDAREDMA KGEIDYVFIR KAPTKEEVME LVKRGEVYSP KTTRHVLPFN PDKIDVKLEE
LF
