Reviewed, UniProtKB/Swiss-Prot P0ABH9 (CLPA_ECOLI)

Names and origin

Protein names

Recommended name:
    ATP-dependent Clp protease ATP-binding subunit clpA

Gene names

Name:	clpA
Synonyms:	lopD
Ordered Locus Names:	b0882, JW0866

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	758 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	ATP-dependent specificity component of the clpP protease. It directs the protease to specific substrates. The primary function of the clpA-clpP complex appears to be the degradation of unfolded or abnormal proteins.
Subunit structure	Twelve clpP subunits assemble into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. In the presence of ATP, clpP subunits interact with the clpP structure to form a 750 kDa complex that exhibits ATP-dependent proteolytic activity. Binds to clpS.
Sequence similarities	Belongs to the clpA/clpB family.

Ontologies

Keywords
Domain	Repeat
Ligand	ATP-binding Nucleotide-binding
Molecular function	Chaperone
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	protein metabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-triphosphatase activity Inferred from electronic annotation. Source: InterPro protein binding Ref.10 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
clpS	P0A8Q6	2	EBI-546140,EBI-561456

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 758

758

ATP-dependent Clp protease ATP-binding subunit clpA

PRO_0000191079

Regions

Nucleotide binding

214 – 221

8

ATP Potential

Nucleotide binding

495 – 502

8

ATP Potential

Region

169 – 417

249

I

Region

421 – 609

189

II

Experimental info

Sequence conflict

367

1

A → G in AAA23583. Ref.1

Sequence conflict

411

1

L → V in AAA23583. Ref.1

Sequence conflict

533

1

L → V in AAA23583. Ref.1

Secondary structure

1

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758

Helix Strand Turn

Details...

Helix

4 – 20

17

Beta strand

22 – 25

4

Helix

27 – 34

8

Helix

38 – 46

9

Helix

51 – 65

15

Helix

82 – 96

15

Beta strand

97 – 99

3

Helix

105 – 112

8

Helix

119 – 126

8

Helix

131 – 139

9

Beta strand

171 – 173

3

Helix

176 – 181

6

Helix

192 – 202

11

Beta strand

204 – 207

4

Beta strand

209 – 213

5

Helix

220 – 233

14

Helix

238 – 240

3

Beta strand

244 – 247

4

Helix

263 – 274

12

Beta strand

275 – 278

4

Beta strand

280 – 284

5

Turn

285 – 292

8

Beta strand

296 – 298

3

Helix

300 – 307

8

Beta strand

311 – 313

3

Beta strand

317 – 322

6

Helix

324 – 328

5

Helix

329 – 333

5

Helix

338 – 340

3

Beta strand

341 – 345

5

Helix

351 – 369

19

Helix

375 – 388

14

Helix

396 – 411

16

Beta strand

412 – 414

3

Helix

423 – 433

11

Beta strand

441 – 444

4

Helix

445 – 456

12

Turn

457 – 459

3

Helix

464 – 478

15

Beta strand

488 – 494

7

Helix

501 – 512

12

Beta strand

515 – 520

6

Helix

521 – 523

3

Beta strand

525 – 528

4

Beta strand

531 – 533

3

Helix

541 – 545

5

Helix

548 – 555

8

Beta strand

557 – 564

8

Helix

566 – 568

3

Helix

571 – 583

13

Beta strand

584 – 588

5

Turn

589 – 591

3

Beta strand

592 – 595

4

Beta strand

599 – 605

7

Helix

629 – 635

7

Helix

638 – 641

4

Beta strand

645 – 649

5

Helix

655 – 675

21

Beta strand

678 – 682

5

Helix

684 – 694

11

Turn

697 – 699

3

Turn

701 – 703

3

Helix

704 – 712

9

Helix

714 – 716

3

Helix

717 – 722

6

Turn

724 – 727

4

Beta strand

729 – 736

8

Turn

737 – 740

4

Beta strand

741 – 748

8

Sequences

	Sequence		Length	Mass (Da)
	P0ABH9-1 [UniParc]. Last modified October 25, 2005. Version 1. Checksum: 0C96A2EB64A9F7DC	FASTA	758	84,207
	10 20 30 40 50 60 MLNQELELSL NMAFARAREH RHEFMTVEHL LLALLSNPSA REALEACSVD LVALRQELEA 70 80 90 100 110 120 FIEQTTPVLP ASEEERDTQP TLSFQRVLQR AVFHVQSSGR NEVTGANVLV AIFSEQESQA 130 140 150 160 170 180 AYLLRKHEVS RLDVVNFISH GTRKDEPTQS SDPGSQPNSE EQAGGEERME NFTTNLNQLA 190 200 210 220 230 240 RVGGIDPLIG REKELERAIQ VLCRRRKNNP LLVGESGVGK TAIAEGLAWR IVQGDVPEVM 250 260 270 280 290 300 ADCTIYSLDI GSLLAGTKYR GDFEKRFKAL LKQLEQDTNS ILFIDEIHTI IGAGAASGGQ 310 320 330 340 350 360 VDAANLIKPL LSSGKIRVIG STTYQEFSNI FEKDRALARR FQKIDITEPS IEETVQIING 370 380 390 400 410 420 LKPKYEAHHD VRYTAKAVRA AVELAVKYIN DRHLPDKAID VIDEAGARAR LMPVSKRKKT 430 440 450 460 470 480 VNVADIESVV ARIARIPEKS VSQSDRDTLK NLGDRLKMLV FGQDKAIEAL TEAIKMARAG 490 500 510 520 530 540 LGHEHKPVGS FLFAGPTGVG KTEVTVQLSK ALGIELLRFD MSEYMERHTV SRLIGAPPGY 550 560 570 580 590 600 VGFDQGGLLT DAVIKHPHAV LLLDEIEKAH PDVFNILLQV MDNGTLTDNN GRKADFRNVV 610 620 630 640 650 660 LVMTTNAGVR ETERKSIGLI HQDNSTDAME EIKKIFTPEF RNRLDNIIWF DHLSTDVIHQ 670 680 690 700 710 720 VVDKFIVELQ VQLDQKGVSL EVSQEARNWL AEKGYDRAMG ARPMARVIQD NLKKPLANEL 730 740 750 LFGSLVDGGQ VTVALDKEKN ELTYGFQSAQ KHKAEAAH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate." Gottesman S., Clark W.P., Maurizi M.R. J. Biol. Chem. 265:7886-7893(1990) [PubMed: 2186030] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[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]	"The two-component, ATP-dependent Clp protease of Escherichia coli. Purification, cloning, and mutational analysis of the ATP-binding component." Katayama Y., Gottesman S., Pumphrey J., Rudikoff S., Clark W.P., Maurizi M.R. J. Biol. Chem. 263:15226-15236(1988) [PubMed: 3049606] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-28, PARTIAL PROTEIN SEQUENCE. Strain: SG1110.
[6]	"Structure and expression of the infA operon encoding translational initiation factor IF1. Transcriptional control by growth rate." Cummings H.S., Sands J.F., Foreman P.C., Fraser J., Hershey J.W.B. J. Biol. Chem. 266:16491-16498(1991) [PubMed: 1909328] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 511-758.
[7]	"Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes." Gottesman S., Squires C., Pichersky E., Carrington M., Hobbs M., Mattick J.S., Dalrymple B., Kuramitsu H., Shiroza T., Foster T., Clark W.P., Ross B., Squires C.L., Maurizi M.R. Proc. Natl. Acad. Sci. U.S.A. 87:3513-3517(1990) [PubMed: 2185473] [Abstract] Cited for: SIMILARITY TO OTHER CLPAB LIKE PROTEINS.
[8]	"Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease." Guo F., Maurizi M.R., Esser L., Xia D. J. Biol. Chem. 277:46743-46752(2002) [PubMed: 12205096] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-143.
[9]	"Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA." Zeth K., Ravelli R.B., Paal K., Cusack S., Bukau B., Dougan D.A. Nat. Struct. Biol. 9:906-911(2002) [PubMed: 12426582] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-146 IN COMPLEX WITH CLPS.
[10]	"Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA." Guo F., Esser L., Singh S.K., Maurizi M.R., Xia D. J. Biol. Chem. 277:46753-46762(2002) [PubMed: 12235156] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 1-143 IN COMPLEX WITH CLPS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M31045 Genomic DNA. Translation: AAA23583.1.
U00096 Genomic DNA. Translation: AAC73969.1.
AP009048 Genomic DNA. Translation: BAA35601.1.
M23220 Genomic DNA. Translation: AAA23582.1.

PIR

SUECCA. B64827.

RefSeq

AP_001513.1.
NP_415403.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K6K	X-ray	1.80	A	1-143	[»]
1KSF	X-ray	2.60	X	1-758	[»]
1LZW	X-ray	2.50	B	1-146	[»]
1MBU	X-ray	2.30	A/B	1-142	[»]
1MBV	X-ray	3.30	A	1-142	[»]
1MBX	X-ray	2.25	A/B	1-142	[»]
1MG9	X-ray	2.30	B	1-146	[»]
1R6B	X-ray	2.25	X	1-758	[»]
1R6C	X-ray	2.15	X	1-143	[»]
1R6O	X-ray	2.25	A/B	1-143	[»]
1R6Q	X-ray	2.35	A/B	1-143	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0ABH9. 70 interactions.

STRING

P0ABH9.

Genome annotation databases

GeneID

945764.

GenomeReviews

Gene locus JW0866 in contig AP009048_GR.
Gene locus b0882 in contig U00096_GR.

KEGG

ecj:JW0866.
eco:b0882.

Organism-specific databases

EchoBASE

EB0154.

EcoGene

EG10156. clpA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0ABH9.

OMA

KFLMQLE

Enzyme and pathway databases

BioCyc

EcoCyc:EG10156-MON.
ECOL168927:B0882-MON.

Gene expression databases

Genevestigator

P0ABH9.

Family and domain databases

InterPro

IPR003593. ATPase_AAA+_core.
IPR013093. ATPase_AAA-2.
IPR003959. ATPase_AAA_core.
IPR018368. Chaperonin_ClpA/B_CS.
IPR001270. Chaprnin_clpA/B.
IPR019489. Clp_ATPase_C.
IPR004176. Clp_N.
IPR013461. ClpA.
[Graphical view]

Pfam

PF00004. AAA. 1 hit.
PF07724. AAA_2. 1 hit.
PF02861. Clp_N. 1 hit.
PF10431. ClpB_D2-small. 1 hit.
[Graphical view]

PRINTS

PR00300. CLPPROTEASEA.

SMART

SM00382. AAA. 2 hits.
[Graphical view]

TIGRFAMs

TIGR02639. ClpA. 1 hit.

PROSITE

PS00870. CLPAB_1. 1 hit.
PS00871. CLPAB_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CLPA_ECOLI

Accession

Primary (citable) accession number: P0ABH9
Secondary accession number(s): P15716, P77686

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	October 25, 2005
Last modified:	November 24, 2009
This is version 36 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)