Reviewed, UniProtKB/Swiss-Prot P69441 (KAD_ECOLI)

Names and origin

Protein names

Recommended name:
    Adenylate kinase
      Short name=AK
    EC=2.7.4.3
Alternative name(s):
    ATP-AMP transphosphorylase

Gene names

Name:	adk
Synonyms:	dnaW, plsA
Ordered Locus Names:	b0474, JW0463

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	214 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. HAMAP MF_00235
Catalytic activity	ATP + AMP = 2 ADP. HAMAP MF_00235
Pathway	Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. HAMAP MF_00235
Subunit structure	Monomer. HAMAP MF_00235
Subcellular location	Cytoplasm HAMAP MF_00235.
Domain	Consists of three domains, a large central CORE domain and two small peripheral domains, AMP binding and LID. The LID domain closes over the site of phosphoryl transfer upon ATP binding. HAMAP MF_00235
Sequence similarities	Belongs to the adenylate kinase family.
Biophysicochemical properties	Kinetic parameters: KM=51 µM for ATP (at pH 7.4 and 30 degrees Celsius) HAMAP MF_00235 KM=38 µM for AMP (at pH 7.4 and 30 degrees Celsius) KM=92 µM for ADP (at pH 7.4 and 30 degrees Celsius) Vmax=1020 µmol/min/mg enzyme for the forward reaction (at pH 7.4 and 30 degrees Celsius) Vmax=605 µmol/min/mg enzyme for the reverse reaction (at pH 7.4 and 30 degrees Celsius) Temperature dependence: Optimum temperature is 45 degrees Celsius. Thermostable. Is half-inactivated at 52 degrees Celsius.

Ontologies

Keywords
Biological process	Nucleotide biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	purine ribonucleotide biosynthetic process Inferred from mutant phenotype. Source: UniProtKB purine ribonucleotide interconversion Inferred from mutant phenotype. Source: UniProtKB
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	AMP binding Inferred from direct assay. Source: UniProtKB ATP binding Inferred from direct assay. Source: UniProtKB adenylate kinase activity Inferred from direct assay. Source: UniProtKB magnesium ion binding Inferred from direct assay. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rpoC	P0A8T7	1	EBI-543592,EBI-543604
ybdL	P77806	1	EBI-543592,EBI-543661

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 214

214

Adenylate kinase HAMAP MF_00235

PRO_0000158767

Regions

Nucleotide binding

7 – 15

9

ATP HAMAP MF_00235

Nucleotide binding

31 – 59

29

AMP HAMAP MF_00235

Region

122 – 159

38

LID HAMAP MF_00235

Amino acid modifications

Modified residue

192

1

N6-acetyllysine Ref.13

Experimental info

Mutagenesis

9

1

P → G: No loss of enzyme activity.

Mutagenesis

10

1

G → V: No loss of enzyme activity.

Mutagenesis

13

1

K → Q: Drastic reduction in enzyme activity.

Secondary structure

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214

Helix Strand Turn

Details...

Beta strand

2 – 8

7

Helix

13 – 24

12

Beta strand

28 – 30

3

Helix

31 – 41

11

Turn

44 – 46

3

Helix

47 – 49

3

Helix

50 – 55

6

Helix

61 – 73

13

Helix

75 – 79

5

Beta strand

81 – 85

5

Helix

90 – 98

9

Beta strand

104 – 110

7

Helix

113 – 115

3

Helix

116 – 121

6

Beta strand

123 – 125

3

Turn

127 – 129

3

Beta strand

132 – 134

3

Turn

135 – 137

3

Turn

147 – 149

3

Helix

161 – 174

14

Turn

175 – 177

3

Helix

178 – 187

10

Beta strand

190 – 197

8

Helix

202 – 213

12

Sequences

	Sequence		Length	Mass (Da)
	P69441-1 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: BB917C84000A80EE	FASTA	214	23,586
	10 20 30 40 50 60 MRIILLGAPG AGKGTQAQFI MEKYGIPQIS TGDMLRAAVK SGSELGKQAK DIMDAGKLVT 70 80 90 100 110 120 DELVIALVKE RIAQEDCRNG FLLDGFPRTI PQADAMKEAG INVDYVLEFD VPDELIVDRI 130 140 150 160 170 180 VGRRVHAPSG RVYHVKFNPP KVEGKDDVTG EELTTRKDDQ EETVRKRLVE YHQMTAPLIG 190 200 210 YYSKEAEAGN TKYAKVDGTK PVAEVRADLE KILG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli." Brune M., Schumann R., Wittinghofer F. Nucleic Acids Res. 13:7139-7151(1985) [PubMed: 2997739] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Eukaryotic Mr 83,000 heat shock protein has a homologue in Escherichia coli." Bardwell J.C.A., Craig E.A. Proc. Natl. Acad. Sci. U.S.A. 84:5177-5181(1987) [PubMed: 3299380] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-5.
[6]	"Isolation and characterization of visible light-sensitive mutants of Escherichia coli K12." Miyamoto K., Nakahigashi K., Nishimura K., Inokuchi H. J. Mol. Biol. 219:393-398(1991) [PubMed: 2051480] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 108-214.
[7]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[8]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-11. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[9]	"Protein identification with N and C-terminal sequence tags in proteome projects." Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C., Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L., Hochstrasser D.F. J. Mol. Biol. 278:599-608(1998) [PubMed: 9600841] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-4. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[10]	"Mutations in the nucleotide binding loop of adenylate kinase of Escherichia coli." Reinstein J., Brune M., Wittinghofer A. Biochemistry 27:4712-4720(1988) [PubMed: 2844237] [Abstract] Cited for: MUTAGENESIS.
[11]	"Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli." Reinstein J., Schlichting I., Wittinghofer A. Biochemistry 29:7451-7459(1990) [PubMed: 2223776] [Abstract] Cited for: MUTAGENESIS.
[12]	"A new subfamily of short bacterial adenylate kinases with the Mycobacterium tuberculosis enzyme as a model: a predictive and experimental study." Munier-Lehmann H., Burlacu-Miron S., Craescu C.T., Mantsch H.H., Schultz C.P. Proteins 36:238-248(1999) [PubMed: 10398370] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[13]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-192, MASS SPECTROMETRY.
[14]	"Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9-A resolution. A model for a catalytic transition state." Mueller C.W., Schulz G.E. J. Mol. Biol. 224:159-177(1992) [PubMed: 1548697] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH THE INHIBITOR AP5A.
[15]	"Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop." Mueller C.W., Schulz G.E. Proteins 15:42-49(1993) [PubMed: 8451239] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF MUTANTS PRO-9 AND GLY-10 IN COMPLEX WITH THE INHIBITOR AP5A.
[16]	"The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP." Berry M.B., Meador B., Bilderback T., Liang P., Glaser M., Phillips G.N. Jr. Proteins 19:183-198(1994) [PubMed: 7937733] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEX WITH AMP AND AMPPNP.
[17]	"Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding." Mueller C.W., Schlauderer G.J., Reinstein J., Schulz G.E. Structure 4:147-156(1996) [PubMed: 8805521] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). Strain: K12.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X03038 Genomic DNA. Translation: CAA26840.1.
U82664 Genomic DNA. Translation: AAB40228.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73576.1.
AP009048 Genomic DNA. Translation: BAE76253.1.
M38777 Genomic DNA. Translation: AAA23461.1.
D90259 Genomic DNA. Translation: BAA14303.1.

PIR

KIECA. A24275.

RefSeq

AP_001123.1.
NP_415007.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AKE	X-ray	2.00	A/B	1-214	[»]
1ANK	X-ray	2.00	A/B	1-214	[»]
1E4V	X-ray	1.85	A/B	1-214	[»]
1E4Y	X-ray	1.85	A/B	1-214	[»]
2ECK	X-ray	2.80	A/B	1-214	[»]
3HPQ	X-ray	2.00	A/B	1-214	[»]
3HPR	X-ray	2.00	A/B	1-214	[»]
4AKE	X-ray	2.20	A/B	1-214	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P69441. 13 interactions.

STRING

P69441.

PTM databases

PhosSite

P69441.

2-D gel databases

SWISS-2DPAGE

P69441.

ECO2DBASE

F026.0. 6TH EDITION.

Genome annotation databases

GeneID

945097.

GenomeReviews

Gene locus JW0463 in contig AP009048_GR.
Gene locus b0474 in contig U00096_GR.

KEGG

ecj:JW0463.
eco:b0474.

Organism-specific databases

EchoBASE

EB0031.

EcoGene

EG10032. adk.

CMR

Search...

Phylogenomic databases

eggNOG

COG0563.

HOGENOM

HBG630208.

OMA

CANGFLF.

Enzyme and pathway databases

BioCyc

EcoCyc:ADENYL-KIN-MONOMER.
ECOL168927:B0474-MONOMER.
MetaCyc:ADENYL-KIN-MONOMER.

Gene expression databases

Genevestigator

P69441.

Family and domain databases

HAMAP

MF_00235. Adenylate_kinase_Adk.
[Tree]

InterPro

IPR006259. Adenyl_kin_sub.
IPR000850. Adenylate_kin.
IPR007862. Adenylate_kinase_lid-dom.
[Graphical view]

PANTHER

PTHR23359. Adenylate_kin. 1 hit.

Pfam

PF00406. ADK. 1 hit.
PF05191. ADK_lid. 1 hit.
[Graphical view]

PRINTS

PR00094. ADENYLTKNASE.

TIGRFAMs

TIGR01351. adk. 1 hit.

PROSITE

PS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00131. Adenosine monophosphate.

Entry information

Entry name

KAD_ECOLI

Accession

Primary (citable) accession number: P69441
Secondary accession number(s): P05082, P77123, Q2MBV3

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	February 9, 2010
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)