TDCD_SALTY
ID TDCD_SALTY Reviewed; 402 AA.
AC O06961;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Propionate kinase {ECO:0000255|HAMAP-Rule:MF_01881};
DE EC=2.7.2.15 {ECO:0000255|HAMAP-Rule:MF_01881};
GN Name=tdcD {ECO:0000255|HAMAP-Rule:MF_01881}; Synonyms=oxd-2;
GN OrderedLocusNames=STM3242;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=10498722; DOI=10.1128/jb.181.19.6092-6097.1999;
RA Wei Y., Miller C.G.;
RT "Characterization of a group of anaerobically induced, fnr-dependent genes
RT of Salmonella typhimurium.";
RL J. Bacteriol. 181:6092-6097(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH ATP ANALOGS,
RP SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=16139298; DOI=10.1016/j.jmb.2005.07.069;
RA Simanshu D.K., Savithri H.S., Murthy M.R.;
RT "Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from
RT Salmonella typhimurium: comparison with members of acetate and sugar
RT kinase/heat shock cognate 70/actin superfamily.";
RL J. Mol. Biol. 352:876-892(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH ATP ANALOGS.
RX PubMed=17894350; DOI=10.1002/prot.21626;
RA Simanshu D.K., Savithri H.S., Murthy M.R.;
RT "Crystal structures of Salmonella typhimurium propionate kinase and its
RT complex with Ap4A: evidence for a novel Ap4A synthetic activity.";
RL Proteins 70:1379-1388(2008).
CC -!- FUNCTION: Catalyzes the conversion of propionyl phosphate and ADP to
CC propionate and ATP. It can also use acetyl phosphate as phosphate group
CC acceptor.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + propanoate = ADP + propanoyl phosphate;
CC Xref=Rhea:RHEA:23148, ChEBI:CHEBI:17272, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:58933, ChEBI:CHEBI:456216; EC=2.7.2.15;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01881};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01881};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=112 uM for ATP (at 25 degrees Celsius and pH 7.5)
CC {ECO:0000269|PubMed:16139298};
CC KM=2.3 mM for propionate (at 25 degrees Celsius and pH 7.5)
CC {ECO:0000269|PubMed:16139298};
CC KM=26.9 mM for acetate (at 25 degrees Celsius and pH 7.5)
CC {ECO:0000269|PubMed:16139298};
CC -!- PATHWAY: Amino-acid degradation; L-threonine degradation via propanoate
CC pathway; propanoate from L-threonine: step 4/4. {ECO:0000255|HAMAP-
CC Rule:MF_01881}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01881,
CC ECO:0000269|PubMed:16139298}.
CC -!- SIMILARITY: Belongs to the acetokinase family. TdcD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01881}.
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DR EMBL; U89718; AAB53419.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL22115.1; -; Genomic_DNA.
DR RefSeq; NP_462156.1; NC_003197.2.
DR RefSeq; WP_001001853.1; NC_003197.2.
DR PDB; 1X3M; X-ray; 2.20 A; A=2-402.
DR PDB; 1X3N; X-ray; 2.30 A; A=2-402.
DR PDB; 2E1Y; X-ray; 2.60 A; A=2-402.
DR PDB; 2E1Z; X-ray; 1.98 A; A=2-402.
DR PDB; 2E20; X-ray; 2.40 A; A=2-402.
DR PDB; 4FWK; X-ray; 2.80 A; A=2-402.
DR PDB; 4FWL; X-ray; 2.40 A; A=2-397.
DR PDB; 4FWM; X-ray; 2.95 A; A=2-397.
DR PDB; 4FWN; X-ray; 3.00 A; A=2-402.
DR PDB; 4FWO; X-ray; 2.90 A; A=2-402.
DR PDB; 4FWP; X-ray; 2.50 A; A=2-402.
DR PDB; 4FWQ; X-ray; 2.65 A; A=2-402.
DR PDB; 4FWR; X-ray; 3.00 A; A=2-402.
DR PDB; 4FWS; X-ray; 2.69 A; A=2-402.
DR PDB; 4XH1; X-ray; 2.00 A; A=2-397.
DR PDB; 4XH4; X-ray; 1.80 A; A=1-402.
DR PDB; 4XH5; X-ray; 2.11 A; A=4-397.
DR PDBsum; 1X3M; -.
DR PDBsum; 1X3N; -.
DR PDBsum; 2E1Y; -.
DR PDBsum; 2E1Z; -.
DR PDBsum; 2E20; -.
DR PDBsum; 4FWK; -.
DR PDBsum; 4FWL; -.
DR PDBsum; 4FWM; -.
DR PDBsum; 4FWN; -.
DR PDBsum; 4FWO; -.
DR PDBsum; 4FWP; -.
DR PDBsum; 4FWQ; -.
DR PDBsum; 4FWR; -.
DR PDBsum; 4FWS; -.
DR PDBsum; 4XH1; -.
DR PDBsum; 4XH4; -.
DR PDBsum; 4XH5; -.
DR AlphaFoldDB; O06961; -.
DR SMR; O06961; -.
DR STRING; 99287.STM3242; -.
DR PaxDb; O06961; -.
DR EnsemblBacteria; AAL22115; AAL22115; STM3242.
DR GeneID; 1254765; -.
DR KEGG; stm:STM3242; -.
DR PATRIC; fig|99287.12.peg.3438; -.
DR HOGENOM; CLU_020352_0_1_6; -.
DR OMA; IHYLYSI; -.
DR PhylomeDB; O06961; -.
DR BioCyc; SENT99287:STM3242-MON; -.
DR BRENDA; 2.7.2.15; 5542.
DR SABIO-RK; O06961; -.
DR UniPathway; UPA00052; UER00510.
DR EvolutionaryTrace; O06961; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008776; F:acetate kinase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008980; F:propionate kinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006083; P:acetate metabolic process; IBA:GO_Central.
DR GO; GO:0070689; P:L-threonine catabolic process to propionate; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00020; Acetate_kinase; 1.
DR HAMAP; MF_01881; Propion_kin_subfam1; 1.
DR InterPro; IPR004372; Ac/propionate_kinase.
DR InterPro; IPR000890; Aliphatic_acid_kin_short-chain.
DR InterPro; IPR023865; Aliphatic_acid_kinase_CS.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR024917; Propionate_kinase.
DR PANTHER; PTHR21060; PTHR21060; 1.
DR PANTHER; PTHR21060:SF17; PTHR21060:SF17; 1.
DR Pfam; PF00871; Acetate_kinase; 1.
DR PIRSF; PIRSF000722; Acetate_prop_kin; 1.
DR PRINTS; PR00471; ACETATEKNASE.
DR SUPFAM; SSF53067; SSF53067; 2.
DR TIGRFAMs; TIGR00016; ackA; 1.
DR PROSITE; PS01075; ACETATE_KINASE_1; 1.
DR PROSITE; PS01076; ACETATE_KINASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..402
FT /note="Propionate kinase"
FT /id="PRO_0000107656"
FT ACT_SITE 143
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT BINDING 18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT BINDING 86
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT BINDING 175
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 203..207
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 278..280
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 326..330
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT BINDING 381
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT SITE 175
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT SITE 236
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01881"
FT CONFLICT 135..142
FT /note="AVRQVAVF -> GRASGGGI (in Ref. 1; AAB53419)"
FT /evidence="ECO:0000305"
FT STRAND 6..12
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 17..23
FT /evidence="ECO:0007829|PDB:4XH4"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 29..37
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 40..48
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 60..73
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 80..88
FT /evidence="ECO:0007829|PDB:4XH4"
FT TURN 91..93
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 102..111
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 116..132
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 136..142
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 161..167
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 176..190
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:1X3M"
FT STRAND 198..214
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 217..222
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 242..252
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 256..265
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 268..273
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 279..287
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 291..312
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:2E20"
FT STRAND 320..324
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 325..330
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 332..340
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 341..345
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 351..355
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 358..360
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:4XH4"
FT STRAND 371..376
FT /evidence="ECO:0007829|PDB:4XH4"
FT HELIX 381..392
FT /evidence="ECO:0007829|PDB:4XH4"
SQ SEQUENCE 402 AA; 43718 MW; EF387E43054FCAB3 CRC64;
MNEFPVVLVI NCGSSSIKFS VLDVATCDVL MAGIADGMNT ENAFLSINGD KPINLAHSNY
EDALKAIAFE LEKRDLTDSV ALIGHRIAHG GELFTQSVII TDEIIDNIRR VSPLAPLHNY
ANLSGIDAAR HLFPAVRQVA VFDTSFHQTL APEAYLYGLP WEYFSSLGVR RYGFHGTSHR
YVSRRAYELL DLDEKDSGLI VAHLGNGASI CAVRNGQSVD TSMGMTPLEG LMMGTRSGDV
DFGAMAWIAK ETGQTLSDLE RVVNKESGLL GISGLSSDLR VLEKAWHEGH ERARLAIKTF
VHRIARHIAG HAASLHRLDG IIFTGGIGEN SVLIRQLVIE HLGVLGLTLD VEMNKQPNSH
GERIISANPS QVICAVIPTN EEKMIALDAI HLGNVKAPVE FA
