KAD_BACSU
ID KAD_BACSU Reviewed; 217 AA.
AC P16304;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 2.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Adenylate kinase {ECO:0000255|HAMAP-Rule:MF_00235};
DE Short=AK {ECO:0000255|HAMAP-Rule:MF_00235};
DE EC=2.7.4.3 {ECO:0000255|HAMAP-Rule:MF_00235};
DE AltName: Full=ATP-AMP transphosphorylase {ECO:0000255|HAMAP-Rule:MF_00235};
DE AltName: Full=ATP:AMP phosphotransferase {ECO:0000255|HAMAP-Rule:MF_00235};
DE AltName: Full=Adenylate monophosphate kinase {ECO:0000255|HAMAP-Rule:MF_00235};
DE AltName: Full=Superoxide-inducible protein 16;
DE Short=SOI16;
GN Name=adk {ECO:0000255|HAMAP-Rule:MF_00235}; OrderedLocusNames=BSU01370;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2113521; DOI=10.1093/oxfordjournals.jbchem.a123093;
RA Nakamura K., Nakamura A., Takamatsu H., Yoshikawa H., Yamane K.;
RT "Cloning and characterization of a Bacillus subtilis gene homologous to E.
RT coli secY.";
RL J. Biochem. 107:603-607(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=8635744; DOI=10.1016/0378-1119(95)00757-1;
RA Suh J.-W., Boylan S.A., Oh S.H., Price C.W.;
RT "Genetic and transcriptional organization of the Bacillus subtilis spc-
RT alpha region.";
RL Gene 169:17-23(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-116.
RX PubMed=2139212; DOI=10.1093/nar/18.6.1647;
RA Yoshikawa H., Doi R.H.;
RT "Sequence of the Bacillus subtilis spectinomycin resistance gene region.";
RL Nucleic Acids Res. 18:1647-1647(1990).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-99.
RC STRAIN=168;
RX PubMed=2110998; DOI=10.1111/j.1365-2958.1990.tb00597.x;
RA Suh J.-W., Boylan S.A., Thomas S.M., Dolan K.M., Oliver D.B., Price C.W.;
RT "Isolation of a secY homologue from Bacillus subtilis: evidence for a
RT common protein export pathway in eubacteria.";
RL Mol. Microbiol. 4:305-314(1990).
RN [6]
RP PROTEIN SEQUENCE OF 1-20.
RC STRAIN=168 / IS58;
RX PubMed=9298659; DOI=10.1002/elps.1150180820;
RA Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.;
RT "First steps from a two-dimensional protein index towards a response-
RT regulation map for Bacillus subtilis.";
RL Electrophoresis 18:1451-1463(1997).
RN [7]
RP ZINC ION.
RX PubMed=1554691; DOI=10.1021/bi00127a002;
RA Glaser P., Presecan E., Delepierre M., Surewicz W.K., Mantsch H.H.,
RA Barzu O., Gilles A.M.;
RT "Zinc, a novel structural element found in the family of bacterial
RT adenylate kinases.";
RL Biochemistry 31:3038-3043(1992).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH BI-SUBSTRATE ANALOG
RP AP5A AND ZINC, AND TEMPERATURE DEPENDENCE.
RX PubMed=15100224; DOI=10.1074/jbc.m401865200;
RA Bae E., Phillips G.N. Jr.;
RT "Structures and analysis of highly homologous psychrophilic, mesophilic,
RT and thermophilic adenylate kinases.";
RL J. Biol. Chem. 279:28202-28208(2004).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 1-216 IN COMPLEX WITH
RP BI-SUBSTRATE ANALOG AP5A AND ZINC.
RX PubMed=16713575; DOI=10.1016/j.molcel.2006.04.012;
RA Counago R., Chen S., Shamoo Y.;
RT "In vivo molecular evolution reveals biophysical origins of organismal
RT fitness.";
RL Mol. Cell 22:441-449(2006).
CC -!- FUNCTION: Catalyzes the reversible transfer of the terminal phosphate
CC group between ATP and AMP. Plays an important role in cellular energy
CC homeostasis and in adenine nucleotide metabolism. {ECO:0000255|HAMAP-
CC Rule:MF_00235}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AMP + ATP = 2 ADP; Xref=Rhea:RHEA:12973, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:456215, ChEBI:CHEBI:456216; EC=2.7.4.3;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00235};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius. Thermal denaturation
CC midpoint (Tm) is 47.6 degrees Celsius and is raised to 66.0 degrees
CC Celsius when AK is complexed with the inhibitor Ap5A.
CC {ECO:0000269|PubMed:15100224};
CC -!- PATHWAY: Purine metabolism; AMP biosynthesis via salvage pathway; AMP
CC from ADP: step 1/1. {ECO:0000255|HAMAP-Rule:MF_00235}.
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00235,
CC ECO:0000269|PubMed:16713575}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- INDUCTION: By superoxide.
CC -!- DOMAIN: Consists of three domains, a large central CORE domain and two
CC small peripheral domains, NMPbind and LID, which undergo movements
CC during catalysis. The LID domain closes over the site of phosphoryl
CC transfer upon ATP binding. Assembling and dissambling the active center
CC during each catalytic cycle provides an effective means to prevent ATP
CC hydrolysis. Some bacteria have evolved a zinc-coordinating structure
CC that stabilizes the LID domain. {ECO:0000255|HAMAP-Rule:MF_00235,
CC ECO:0000305|PubMed:15100224, ECO:0000305|PubMed:1554691,
CC ECO:0000305|PubMed:16713575}.
CC -!- SIMILARITY: Belongs to the adenylate kinase family. {ECO:0000255|HAMAP-
CC Rule:MF_00235}.
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DR EMBL; D00619; BAA00496.1; -; Genomic_DNA.
DR EMBL; L47971; AAB06820.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB11913.1; -; Genomic_DNA.
DR EMBL; M31102; AAB59119.1; -; Genomic_DNA.
DR EMBL; X51329; CAA35713.1; -; Genomic_DNA.
DR PIR; JS0492; JS0492.
DR RefSeq; NP_388018.1; NC_000964.3.
DR RefSeq; WP_004399686.1; NZ_JNCM01000029.1.
DR PDB; 1P3J; X-ray; 1.90 A; A=1-217.
DR PDB; 2EU8; X-ray; 1.80 A; A/B=1-216.
DR PDB; 2OO7; X-ray; 1.80 A; A/B=1-217.
DR PDB; 2ORI; X-ray; 1.80 A; A/B=1-216.
DR PDB; 2OSB; X-ray; 1.80 A; A/B=1-216.
DR PDB; 2P3S; X-ray; 1.80 A; A=1-217.
DR PDB; 2QAJ; X-ray; 1.80 A; A/B=1-217.
DR PDB; 3DKV; X-ray; 1.82 A; A=1-217.
DR PDB; 3DL0; X-ray; 1.58 A; A/B=1-216.
DR PDB; 4MKF; X-ray; 1.70 A; A/B=1-217.
DR PDB; 4MKG; X-ray; 1.45 A; A=1-217.
DR PDB; 4MKH; X-ray; 1.50 A; A=1-212.
DR PDB; 4QBF; X-ray; 1.80 A; A=1-217.
DR PDB; 4QBG; X-ray; 1.37 A; B=1-217.
DR PDB; 4TYP; X-ray; 2.90 A; A/B/C/D=1-217.
DR PDB; 4TYQ; X-ray; 1.65 A; A/B=1-217.
DR PDB; 5X6I; X-ray; 2.00 A; A=1-217.
DR PDBsum; 1P3J; -.
DR PDBsum; 2EU8; -.
DR PDBsum; 2OO7; -.
DR PDBsum; 2ORI; -.
DR PDBsum; 2OSB; -.
DR PDBsum; 2P3S; -.
DR PDBsum; 2QAJ; -.
DR PDBsum; 3DKV; -.
DR PDBsum; 3DL0; -.
DR PDBsum; 4MKF; -.
DR PDBsum; 4MKG; -.
DR PDBsum; 4MKH; -.
DR PDBsum; 4QBF; -.
DR PDBsum; 4QBG; -.
DR PDBsum; 4TYP; -.
DR PDBsum; 4TYQ; -.
DR PDBsum; 5X6I; -.
DR AlphaFoldDB; P16304; -.
DR SMR; P16304; -.
DR IntAct; P16304; 1.
DR MINT; P16304; -.
DR STRING; 224308.BSU01370; -.
DR DrugBank; DB01717; Bis(Adenosine)-5'-Pentaphosphate.
DR jPOST; P16304; -.
DR PaxDb; P16304; -.
DR PRIDE; P16304; -.
DR EnsemblBacteria; CAB11913; CAB11913; BSU_01370.
DR GeneID; 938508; -.
DR KEGG; bsu:BSU01370; -.
DR PATRIC; fig|224308.179.peg.140; -.
DR eggNOG; COG0563; Bacteria.
DR InParanoid; P16304; -.
DR OMA; FHNRMRV; -.
DR PhylomeDB; P16304; -.
DR BioCyc; BSUB:BSU01370-MON; -.
DR BRENDA; 2.7.4.3; 658.
DR SABIO-RK; P16304; -.
DR UniPathway; UPA00588; UER00649.
DR EvolutionaryTrace; P16304; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004017; F:adenylate kinase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0044209; P:AMP salvage; IEA:UniProtKB-UniPathway.
DR GO; GO:0009132; P:nucleoside diphosphate metabolic process; IBA:GO_Central.
DR GO; GO:0009123; P:nucleoside monophosphate metabolic process; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR CDD; cd01428; ADK; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00235; Adenylate_kinase_Adk; 1.
DR InterPro; IPR006259; Adenyl_kin_sub.
DR InterPro; IPR000850; Adenylat/UMP-CMP_kin.
DR InterPro; IPR033690; Adenylat_kinase_CS.
DR InterPro; IPR007862; Adenylate_kinase_lid-dom.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR23359; PTHR23359; 1.
DR Pfam; PF05191; ADK_lid; 1.
DR PRINTS; PR00094; ADENYLTKNASE.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01351; adk; 1.
DR PROSITE; PS00113; ADENYLATE_KINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Direct protein sequencing; Kinase;
KW Metal-binding; Nucleotide biosynthesis; Nucleotide-binding;
KW Reference proteome; Transferase; Zinc.
FT CHAIN 1..217
FT /note="Adenylate kinase"
FT /id="PRO_0000158730"
FT REGION 30..59
FT /note="NMP"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT REGION 126..163
FT /note="LID"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 10..15
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 31
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 36
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 57..59
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 85..88
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 92
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 127
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 130
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 133
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 136..137
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 153
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 160
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 171
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT BINDING 199
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00235,
FT ECO:0000269|PubMed:15100224, ECO:0000269|PubMed:16713575"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 31..41
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 44..53
FT /evidence="ECO:0007829|PDB:4QBG"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 61..72
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 90..102
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 109..114
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 117..124
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 127..130
FT /evidence="ECO:0007829|PDB:4QBG"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 136..138
FT /evidence="ECO:0007829|PDB:4QBG"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:4QBG"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:4MKG"
FT HELIX 165..188
FT /evidence="ECO:0007829|PDB:4QBG"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 201..212
FT /evidence="ECO:0007829|PDB:4QBG"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:3DL0"
SQ SEQUENCE 217 AA; 24119 MW; ECB9ECF4F26A1E90 CRC64;
MNLVLMGLPG AGKGTQGERI VEDYGIPHIS TGDMFRAAMK EETPLGLEAK SYIDKGELVP
DEVTIGIVKE RLGKDDCERG FLLDGFPRTV AQAEALEEIL EEYGKPIDYV INIEVDKDVL
MERLTGRRIC SVCGTTYHLV FNPPKTPGIC DKDGGELYQR ADDNEETVSK RLEVNMKQTQ
PLLDFYSEKG YLANVNGQQD IQDVYADVKD LLGGLKK
