Q9RA63 (CLPB_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Chaperone protein ClpB

Gene names

Name:	clpB
Ordered Locus Names:	TTHA1487

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › Thermus thermophilus

Protein attributes

Sequence length	854 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK. Ref.1
Subunit structure	Homohexamer. The oligomerization is ATP-dependent. Ref.5 Ref.6
Subcellular location	Cytoplasm Probable.
Domain	The N-terminal domain probably functions as a substrate-discriminating domain, recruiting aggregated proteins to the ClpB hexamer and/or stabilizing bound proteins. The NBD2 domain is responsible for oligomerization, whereas the NBD1 domain stabilizes the hexamer probably in an ATP-dependent manner. The movement of the coiled-coil domain is essential for ClpB ability to rescue proteins from an aggregated state, probably by pulling apart large aggregated proteins, which are bound between the coiled-coils motifs of adjacent ClpB subunits in the functional hexamer.
Sequence similarities	Belongs to the clpA/clpB family.

Ontologies

Keywords
Biological process	Stress response
Cellular component	Cytoplasm
Domain	Coiled coil Repeat
Ligand	ATP-binding Nucleotide-binding
Molecular function	Chaperone
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein processing Inferred from electronic annotation. Source: InterPro response to heat Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-triphosphatase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 854

854

Chaperone protein ClpB

PRO_0000191195

Regions

Nucleotide binding

198 – 205

8

ATP 1

Nucleotide binding

595 – 602

8

ATP 2

Region

1 – 135

135

N-terminal

Region

151 – 331

181

NBD1

Region

332 – 535

204

Linker

Region

545 – 756

212

NBD2

Region

757 – 854

98

C-terminal

Coiled coil

382 – 516

135

Experimental info

Mutagenesis

167

1

G → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-475. Ref.9

Mutagenesis

204 – 205

2

KT → AA: Loss of ability to bind ATP. Residual ATPase activity.

Mutagenesis

270

1

D → N: No effect on ability to bind ATP. Decrease in ATPase activity. Ref.6

Mutagenesis

271

1

E → Q: No effect on ability to bind ATP. Increase in ATPase activity. Ref.6

Mutagenesis

350

1

V → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-467. Ref.9

Mutagenesis

353

1

G → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-464. Ref.9

Mutagenesis

355

1

R → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-520. Ref.9

Mutagenesis

396

1

L → A: Great decrease in chaperone activity. Retains ATPase activity and oligomerization. Ref.9

Mutagenesis

460

1

L → A: Great decrease in chaperone activity. Retains ATPase activity and oligomerization. Ref.9

Mutagenesis

464

1

R → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-353. Ref.9

Mutagenesis

467

1

Q → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-350. Ref.9

Mutagenesis

475

1

R → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-167. Ref.9

Mutagenesis

520

1

E → C: Great decrease in chaperone activity. Retains ATPase activity and oligomerization; when associated with C-355. Ref.9

Mutagenesis

601 – 602

2

KT → AA: Loss of ability to bind ATP. Residual ATPase activity.

Mutagenesis

667

1

D → N: Decrease in ATPase activity. Ref.6

Mutagenesis

668

1

E → Q: Decrease in ATPase activity. Ref.6

Sequence conflict

96

1

A → G in BAA81745. Ref.1

Sequence conflict

96

1

A → G in BAA96085. Ref.1

Secondary structure

1

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854

Helix Strand Turn

Details...

Helix

8 – 23

16

Beta strand

27 – 29

3

Helix

31 – 38

8

Beta strand

41 – 44

4

Helix

45 – 51

7

Helix

57 – 69

13

Helix

76 – 78

3

Helix

85 – 99

15

Turn

100 – 102

3

Helix

108 – 118

11

Helix

125 – 132

8

Helix

152 – 155

4

Beta strand

156 – 159

4

Helix

160 – 165

6

Helix

176 – 186

11

Beta strand

188 – 191

4

Beta strand

193 – 197

5

Helix

204 – 217

14

Helix

222 – 224

3

Beta strand

228 – 232

5

Helix

234 – 238

5

Helix

246 – 260

15

Turn

261 – 263

3

Beta strand

264 – 271

8

Helix

272 – 274

3

Helix

288 – 296

9

Beta strand

301 – 306

6

Helix

308 – 315

8

Helix

318 – 321

4

Beta strand

324 – 328

5

Helix

334 – 352

19

Helix

358 – 371

14

Helix

379 – 397

19

Helix

401 – 419

19

Helix

429 – 483

55

Helix

486 – 493

8

Helix

496 – 512

17

Beta strand

519 – 521

3

Helix

523 – 531

9

Helix

537 – 540

4

Helix

544 – 550

7

Helix

552 – 557

6

Helix

564 – 579

16

Beta strand

584 – 586

3

Beta strand

588 – 595

8

Beta strand

597 – 600

4

Helix

601 – 613

13

Helix

616 – 618

3

Beta strand

619 – 623

5

Helix

624 – 626

3

Helix

632 – 637

6

Beta strand

641 – 643

3

Turn

644 – 648

5

Helix

651 – 658

8

Beta strand

660 – 667

8

Helix

669 – 671

3

Helix

674 – 686

13

Beta strand

687 – 690

4

Beta strand

692 – 694

3

Beta strand

696 – 698

3

Beta strand

702 – 709

8

Helix

712 – 716

5

Turn

717 – 720

4

Beta strand

725 – 727

3

Helix

728 – 731

4

Helix

733 – 739

7

Helix

742 – 745

4

Beta strand

749 – 753

5

Helix

759 – 769

11

Helix

771 – 778

8

Turn

779 – 781

3

Beta strand

783 – 786

4

Helix

788 – 797

10

Turn

801 – 803

3

Turn

805 – 807

3

Helix

808 – 815

8

Helix

817 – 825

9

Beta strand

827 – 829

3

Beta strand

834 – 839

6

Beta strand

841 – 847

7

Sequences

	Sequence		Length	Mass (Da)
	Q9RA63 [UniParc]. Last modified May 24, 2005. Version 2. Checksum: FB9A39BB040363E0	FASTA	854	96,254
	10 20 30 40 50 60 MNLERWTQAA REALAQAQVL AQRMKHQAID LPHLWAVLLK DERSLAWRLL EKAGADPKAL 70 80 90 100 110 120 KELQERELAR LPKVEGAEVG QYLTSRLSGA LNRAEALMEE LKDRYVAVDT LVLALAEATP 130 140 150 160 170 180 GLPGLEALKG ALKELRGGRT VQTEHAESTY NALEQYGIDL TRLAAEGKLD PVIGRDEEIR 190 200 210 220 230 240 RVIQILLRRT KNNPVLIGEP GVGKTAIVEG LAQRIVKGDV PEGLKGKRIV SLQMGSLLAG 250 260 270 280 290 300 AKYRGEFEER LKAVIQEVVQ SQGEVILFID ELHTVVGAGK AEGAVDAGNM LKPALARGEL 310 320 330 340 350 360 RLIGATTLDE YREIEKDPAL ERRFQPVYVD EPTVEETISI LRGLKEKYEV HHGVRISDSA 370 380 390 400 410 420 IIAAATLSHR YITERRLPDK AIDLIDEAAA RLRMALESAP EEIDALERKK LQLEIEREAL 430 440 450 460 470 480 KKEKDPDSQE RLKAIEAEIA KLTEEIAKLR AEWEREREIL RKLREAQHRL DEVRREIELA 490 500 510 520 530 540 ERQYDLNRAA ELRYGELPKL EAEVEALSEK LRGARFVRLE VTEEDIAEIV SRWTGIPVSK 550 560 570 580 590 600 LLEGEREKLL RLEEELHKRV VGQDEAIRAV ADAIRRARAG LKDPNRPIGS FLFLGPTGVG 610 620 630 640 650 660 KTELAKTLAA TLFDTEEAMI RIDMTEYMEK HAVSRLIGAP PGYVGYEEGG QLTEAVRRRP 670 680 690 700 710 720 YSVILFDEIE KAHPDVFNIL LQILDDGRLT DSHGRTVDFR NTVIILTSNL GSPLILEGLQ 730 740 750 760 770 780 KGWPYERIRD EVFKVLQQHF RPEFLNRLDE IVVFRPLTKE QIRQIVEIQL SYLRARLAEK 790 800 810 820 830 840 RISLELTEAA KDFLAERGYD PVFGARPLRR VIQRELETPL AQKILAGEVK EGDRVQVDVG 850 PAGLVFAVPA RVEA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Heat-inactivated proteins are rescued by the DnaK/J-GrpE set and ClpB chaperones." Motohashi K., Watanabe Y.H., Yohda M., Yoshida M. Proc. Natl. Acad. Sci. U.S.A. 96:7184-7189(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Complete genome sequence of Thermus thermophilus HB8." Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S. Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HB8 / ATCC 27634 / DSM 579.
[3]	"The functional cycle and regulation of the Thermus thermophilus DnaK chaperone system." Klostermeier D., Seidel R., Reinstein J. J. Mol. Biol. 287:511-525(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-508.
[4]	"Heat-inactivated proteins managed by DnaKJ-GrpE-ClpB chaperones are released as a chaperonin-recognizable non-native form." Watanabe Y.H., Motohashi K., Taguchi H., Yoshida M. J. Biol. Chem. 275:12388-12392(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH THE DNAK-DNAJ-GRPE CHAPERONE SYSTEM.
[5]	"The chaperone function of ClpB from Thermus thermophilus depends on allosteric interactions of its two ATP-binding sites." Schlee S., Groemping Y., Herde P., Seidel R., Reinstein J. J. Mol. Biol. 306:889-899(2001) [PubMed] [Europe PMC] [Abstract] Cited for: PRELIMINARY CHARACTERIZATION OF SUBUNIT.
[6]	"Roles of the two ATP binding sites of ClpB from Thermus thermophilus." Watanabe Y.H., Motohashi K., Yoshida M. J. Biol. Chem. 277:5804-5809(2002) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, MUTAGENESIS OF 204-LYS-THR-205; ASP-270; GLU-271; 601-LYS-THR-602; ASP-667 AND GLU-668.
[7]	"A chaperone network for the resolubilization of protein aggregates: direct interaction of ClpB and DnaK." Schlee S., Beinker P., Akhrymuk A., Reinstein J. J. Mol. Biol. 336:275-285(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH DNAK.
[8]	"Crystallization and preliminary X-ray crystallographic analysis of the Hsp100 protein clpB from Thermus thermophilus." Lee S., Hisayoshi M., Yoshida M., Tsai F.T.F. Acta Crystallogr. D 59:2334-2336(2003) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION.
[9]	"The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state." Lee S., Sowa M.E., Watanabe Y.H., Sigler P.B., Chiu W., Yoshida M., Tsai F.T.F. Cell 115:229-240(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH AMPPNP, MUTAGENESIS OF GLY-167; VAL-350; GLY-353; ARG-355; LEU-396; LEU-460; ARG-464; GLN-467; ARG-475 AND GLU-520.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB012390 Genomic DNA. Translation: BAA81745.1.
AB032368 Genomic DNA. Translation: BAA96085.1.
AP008226 Genomic DNA. Translation: BAD71310.1.
Y07826 Genomic DNA. Translation: CAA69163.2.

RefSeq

YP_144753.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QVR	X-ray	3.00	A/B/C	1-854	[»]
4FCT	X-ray	4.00	A	545-852	[»]
4FCV	X-ray	3.40	A/B/C	544-852	[»]
4FCW	X-ray	2.35	A/C/F	544-852	[»]
4FD2	X-ray	3.00	A/B/D	545-852	[»]
4HSE	X-ray	2.20	A	142-534	[»]

ProteinModelPortal

Q9RA63.

SMR

Q9RA63. Positions 4-850.

ModBase

Search...

Protein-protein interaction databases

STRING

300852.TTHA1487.

PTM databases

PhosSite

P12101831.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD71310; BAD71310; BAD71310.

GeneID

3167975.

KEGG

ttj:TTHA1487.

PATRIC

23957935. VBITheThe93045_1462.

Phylogenomic databases

eggNOG

COG0542.

HOGENOM

HOG000218211.

KO

K03695.

OMA

DFLTDNM.

ProtClustDB

CLSK444852.

Family and domain databases

Gene3D

1.10.1780.10. 1 hit.

InterPro

IPR003593. AAA+_ATPase.
IPR013093. ATPase_AAA-2.
IPR003959. ATPase_AAA_core.
IPR018368. Chaperonin_ClpA/B_CS.
IPR017730. Chaperonin_ClpB.
IPR001270. Chaprnin_ClpA/B.
IPR019489. Clp_ATPase_C.
IPR004176. Clp_N.
IPR023150. Dbl_Clp-N.
[Graphical view]

Pfam

PF00004. AAA. 1 hit.
PF07724. AAA_2. 1 hit.
PF02861. Clp_N. 2 hits.
PF10431. ClpB_D2-small. 1 hit.
[Graphical view]

PRINTS

PR00300. CLPPROTEASEA.

SMART

SM00382. AAA. 2 hits.
SM01086. ClpB_D2-small. 1 hit.
[Graphical view]

TIGRFAMs

TIGR03346. chaperone_ClpB. 1 hit.

PROSITE

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

ProtoNet

Search...

Other

EvolutionaryTrace

Q9RA63.

Entry information

Entry name

CLPB_THET8

Accession

Primary (citable) accession number: Q9RA63
Secondary accession number(s): P74942, Q5SI87

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 16, 2001
Last sequence update:	May 24, 2005
Last modified:	May 1, 2013
This is version 92 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program