P22259 (PCKA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphoenolpyruvate carboxykinase [ATP]
Short name=PEP carboxykinase
Short name=PEPCK
EC=4.1.1.49

Alternative name(s):
Phosphoenolpyruvate carboxylase

Gene names

Name:	pckA
Synonyms:	pck
Ordered Locus Names:	b3403, JW3366

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	540 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2. HAMAP-Rule MF_00453
Enzyme regulation	Allosterically activated by calcium. Positively regulated by cAMP. HAMAP-Rule MF_00453
Pathway	Carbohydrate biosynthesis; gluconeogenesis. HAMAP-Rule MF_00453
Subunit structure	Monomer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00453.
Sequence similarities	Belongs to the phosphoenolpyruvate carboxykinase [ATP] family.
Mass spectrometry	Molecular mass is 59656 Da from positions 1 - 540. Determined by ESI. Ref.10
Sequence caution	The sequence AAA24301.1 differs from that shown. Reason: Frameshift at position 456.

Ontologies

Keywords
Biological process	Gluconeogenesis
Cellular component	Cytoplasm
Ligand	ATP-binding Calcium Nucleotide-binding
Molecular function	Decarboxylase Lyase
PTM	Acetylation
Technical term	3D-structure Allosteric enzyme Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	gluconeogenesis Inferred from mutant phenotype PubMed 4370531. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP calcium ion binding Inferred from direct assay PubMed 12837799. Source: EcoCyc magnesium ion binding Inferred from direct assay PubMed 8448184. Source: EcoCyc phosphoenolpyruvate carboxykinase (ATP) activity Inferred from direct assay PubMed 6986370. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 540

540

Phosphoenolpyruvate carboxykinase [ATP] HAMAP-Rule MF_00453

PRO_0000203818

Regions

Nucleotide binding

248 – 255

8

ATP HAMAP-Rule MF_00453

Amino acid modifications

Modified residue

87

1

N6-acetyllysine Ref.9

Modified residue

523

1

N6-acetyllysine Ref.9

Experimental info

Mutagenesis

268

1

D → N in PCK51; altered-activity mutant that catalyzes the conversion from oxaloacetate to pyruvate (OAA decarboxylase activity). Ref.6

Mutagenesis

284

1

G → S in PCK53; shows reduced-activity. Ref.6

Sequence conflict

67 – 72

6

PKDKYI → QKISIS in AAA24301. Ref.1

Sequence conflict

192 – 194

3

AFN → R AA sequence Ref.1

Sequence conflict

197 – 203

7

ERMQLIG → DRAHAADC AA sequence Ref.1

Sequence conflict

233

1

C → S in AAA24301. Ref.1

Sequence conflict

252

1

T → N in AAA24301. Ref.1

Sequence conflict

256 – 260

5

TLSTD → AFPR in AAA24301. Ref.1

Sequence conflict

281 – 285

5

FEGGC → LKAAG in AAA24301. Ref.1

Sequence conflict

302 – 307

6

NAIRRD → KLSVVM in AAA24301. Ref.1

Sequence conflict

346

1

K → R in AAA24301. Ref.1

Sequence conflict

354 – 359

6

ATKVIF → GRRLSL in AAA24301. Ref.1

Sequence conflict

363

1

D → H in AAA24301. Ref.1

Sequence conflict

446

1

T → S in AAA24301. Ref.1

Sequence conflict

449

1

R → S in AAA24301. Ref.1

Sequence conflict

460 – 467

8

DAILNGSL → RRHPQRFV Ref.4

Sequence conflict

499

1

T → R Ref.4

Secondary structure

1

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540

Helix Strand Turn

Details...

Turn

5 – 7

3

Helix

9 – 14

6

Beta strand

23 – 26

4

Helix

29 – 37

9

Helix

43 – 45

3

Beta strand

47 – 49

3

Beta strand

55 – 57

3

Helix

67 – 69

3

Beta strand

70 – 73

4

Turn

76 – 81

6

Beta strand

87 – 90

4

Beta strand

95 – 97

3

Helix

99 – 113

15

Beta strand

118 – 128

11

Turn

129 – 131

3

Beta strand

133 – 140

8

Helix

142 – 151

10

Helix

157 – 161

5

Beta strand

166 – 172

7

Turn

178 – 184

7

Beta strand

186 – 188

3

Beta strand

190 – 194

5

Turn

195 – 198

4

Beta strand

199 – 204

6

Helix

209 – 222

14

Helix

224 – 226

3

Beta strand

229 – 231

3

Beta strand

233 – 237

5

Beta strand

243 – 247

5

Helix

254 – 258

5

Beta strand

263 – 269

7

Beta strand

271 – 274

4

Beta strand

277 – 281

5

Beta strand

283 – 288

6

Turn

294 – 296

3

Helix

298 – 302

5

Beta strand

309 – 312

4

Beta strand

314 – 316

3

Turn

317 – 319

3

Beta strand

320 – 322

3

Beta strand

333 – 337

5

Helix

338 – 340

3

Beta strand

341 – 344

4

Beta strand

347 – 352

6

Beta strand

354 – 361

8

Beta strand

370 – 373

4

Helix

376 – 385

10

Beta strand

387 – 391

5

Helix

394 – 396

3

Beta strand

401 – 405

5

Helix

407 – 409

3

Helix

411 – 413

3

Helix

418 – 432

15

Beta strand

435 – 440

6

Beta strand

447 – 449

3

Helix

452 – 463

12

Helix

466 – 469

4

Beta strand

472 – 475

4

Turn

476 – 479

4

Beta strand

480 – 484

5

Helix

491 – 494

4

Helix

496 – 499

4

Beta strand

500 – 502

3

Helix

503 – 521

19

Helix

522 – 524

3

Helix

528 – 533

6

Helix

534 – 536

3

Sequences

	Sequence		Length	Mass (Da)
	P22259 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: A744D90899F6A8A5	FASTA	540	59,643
	10 20 30 40 50 60 MRVNNGLTPQ ELEAYGISDV HDIVYNPSYD LLYQEELDPS LTGYERGVLT NLGAVAVDTG 70 80 90 100 110 120 IFTGRSPKDK YIVRDDTTRD TFWWADKGKG KNDNKPLSPE TWQHLKGLVT RQLSGKRLFV 130 140 150 160 170 180 VDAFCGANPD TRLSVRFITE VAWQAHFVKN MFIRPSDEEL AGFKPDFIVM NGAKCTNPQW 190 200 210 220 230 240 KEQGLNSENF VAFNLTERMQ LIGGTWYGGE MKKGMFSMMN YLLPLKGIAS MHCSANVGEK 250 260 270 280 290 300 GDVAVFFGLS GTGKTTLSTD PKRRLIGDDE HGWDDDGVFN FEGGCYAKTI KLSKEAEPEI 310 320 330 340 350 360 YNAIRRDALL ENVTVREDGT IDFDDGSKTE NTRVSYPIYH IDNIVKPVSK AGHATKVIFL 370 380 390 400 410 420 TADAFGVLPP VSRLTADQTQ YHFLSGFTAK LAGTERGITE PTPTFSACFG AAFLSLHPTQ 430 440 450 460 470 480 YAEVLVKRMQ AAGAQAYLVN TGWNGTGKRI SIKDTRAIID AILNGSLDNA ETFTLPMFNL 490 500 510 520 530 540 AIPTELPGVD TKILDPRNTY ASPEQWQEKA ETLAKLFIDN FDKYTDTPAG AALVAAGPKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of the pckA gene of Escherichia coli K-12: relevance to genetic and allosteric regulation and homology of E. coli phosphoenolpyruvate carboxykinase with the enzymes from Trypanosoma brucei and Saccharomyces cerevisiae." Medina V., Pontarollo R., Glaeske D., Tabel H., Goldie H. J. Bacteriol. 172:7151-7156(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: K12.
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Osmoregulation of gene expression. II. DNA sequence of the envZ gene of the ompB operon of Escherichia coli and characterization of its gene product." Mizuno T., Wurtzel E.T., Inouye M. J. Biol. Chem. 257:13692-13698(1982) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 439-540.
[5]	"The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli." Ramseier T.M., Bledig S., Michotey V., Feghali R., Saier M.H. Jr. Mol. Microbiol. 16:1157-1169(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-39. Strain: K12.
[6]	"A mutant phosphoenolpyruvate carboxykinase in Escherichia coli conferring oxaloacetate decarboxylase activity." Hou S.-Y., Chao Y.-P., Liao J.C. J. Bacteriol. 177:1620-1623(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 242-290, MUTAGENESIS OF ASP-268 AND GLY-284.
[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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[8]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[9]	"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] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-87 AND LYS-523, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[10]	"Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: a new structural family with the P-loop nucleoside triphosphate hydrolase fold." Matte A., Goldie H., Sweet R.M., Delbaere L.T.J. J. Mol. Biol. 256:126-143(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), MASS SPECTROMETRY.
[11]	"Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase." Tari L.W., Matte A., Pugazhenthi U., Goldie H., Delbaere L.T.J. Nat. Struct. Biol. 3:355-363(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[12]	"Mg(2+)-Mn(2+) clusters in enzyme-catalyzed phosphoryl-transfer reactions." Tari L.W., Matte A., Goldie H., Delbaere L.T. Nat. Struct. Biol. 4:990-994(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M59823 Genomic DNA. Translation: AAA24301.1. Frameshift.
U18997 Genomic DNA. Translation: AAA58200.1.
U00096 Genomic DNA. Translation: AAC76428.1.
AP009048 Genomic DNA. Translation: BAE77888.1.
J01656 Unassigned RNA. No translation available.
S76268 Genomic DNA. Translation: AAB33745.2.
S76269 Genomic DNA. Translation: AAB33746.2.
U21325 Genomic DNA. Translation: AAA95999.1.

PIR

F65135.

RefSeq

NP_417862.1. NC_000913.2.
YP_492029.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AQ2	X-ray	1.90	A	1-540	[»]
1AYL	X-ray	1.80	A	1-540	[»]
1K3C	X-ray	2.00	A	1-540	[»]
1K3D	X-ray	2.00	A	1-540	[»]
1OEN	X-ray	1.90	A	1-538	[»]
1OS1	X-ray	1.80	A	1-540	[»]
2OLQ	X-ray	1.94	A	1-540	[»]
2OLR	X-ray	1.60	A	1-540	[»]
2PXZ	X-ray	2.23	X	1-540	[»]
2PY7	X-ray	2.20	X	1-540	[»]

ProteinModelPortal

P22259.

SMR

P22259. Positions 6-540.

ModBase

Search...

Protein-protein interaction databases

IntAct

P22259. 4 interactions.

STRING

511145.b3403.

PTM databases

PhosSite

P0809417.

Proteomic databases

PaxDb

P22259.

PRIDE

P22259.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76428; AAC76428; b3403.
BAE77888; BAE77888; BAE77888.

GeneID

12933187.
945667.

KEGG

ecj:Y75_p3773.
eco:b3403.

PATRIC

32122242. VBIEscCol129921_3498.

Organism-specific databases

EchoBASE

EB0682.

EcoGene

EG10688. pck.

Phylogenomic databases

eggNOG

COG1866.

HOGENOM

HOG000271471.

KO

K01610.

OMA

TRCAYPI.

ProtClustDB

PRK09344.

Enzyme and pathway databases

BioCyc

EcoCyc:PEPCARBOXYKIN-MONOMER.
ECOL316407:JW3366-MONOMER.
MetaCyc:PEPCARBOXYKIN-MONOMER.

UniPathway

UPA00138.

Gene expression databases

Genevestigator

P22259.

Family and domain databases

Gene3D

3.40.449.10. 1 hit.
3.90.228.20. 2 hits.

HAMAP

MF_00453. PEPCK_ATP.

InterPro

IPR001272. PEP_carboxykinase_ATP.
IPR013035. PEP_carboxykinase_C.
IPR008210. PEP_carboxykinase_N.
IPR015994. PEPCK_ATP_CS.
[Graphical view]

Pfam

PF01293. PEPCK_ATP. 1 hit.
[Graphical view]

PIRSF

PIRSF006294. PEP_crbxkin. 1 hit.

SUPFAM

SSF68923. PEP_carboxykinase_N. 1 hit.

TIGRFAMs

TIGR00224. pckA. 1 hit.

PROSITE

PS00532. PEPCK_ATP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P22259.

Entry information

Entry name

PCKA_ECOLI

Accession

Primary (citable) accession number: P22259
Secondary accession number(s): Q2M768

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 131 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program