Primary Citation PubMed: 14567920
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The many faces of protein-protein interactions: A compendium of interface geometry.
(2006) PLoS Comput Biol 2
PubMed: 17009862 | PubMedCentral: PMC1584320 | DOI: 10.1371/journal.pcbi.0020124
The Protein Data Bank ( http://www.pdb.org ) accession numbers for the structures mentioned in this paper are α-amylase from Bacillus licheniformis (1bli), aldehyde oxidoreductase of Desulfovi... rio desulfuricans (1dgj), Allium sativum lectin (1kj1), CO dehydrogenase of Hydrogenophaga pseudoflava (1ffu), DNA clamp loader complex (1sxj), fused domain pair of Scilla campanulata agglutinin (1dlp), guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1) (1i2m), haemagglutinin component (HA1) of the progenitor toxin from Clostridium botulinum (1qxm), Haemophilus ducreyi cytolethal distending toxin (1sr4), ClpB protein (1qvr), molybdenum cofactor-binding domain in CO dehydrogenase from Oligotropha carboxidovorans (1n60), Ran-binding domain complexed with Ran bound to a GTP analogue (1rrp).
Publication Year: 2006
Amyloid oligomer conformation in a group of natively folded proteins.
(2008) PLoS One 3
PubMed: 18800165 | PubMedCentral: PMC2528939 | DOI: 10.1371/journal.pone.0003235
(H) ClpB (Hsp104) [1qvr].
Publication Year: 2008
The AAA+ superfamily of functionally diverse proteins.
(2008) Genome Biol 9
PubMed: 18466635 | PubMedCentral: PMC2643927 | DOI: 10.1186/gb-2008-9-4-216
The amino-terminal (D1) AAA+ modules of ClpB-type proteins are represented by a structure from T. thermophilus (right, PDB 1QVR ).
Motor mechanism for protein threading through Hsp104.
(2009) Mol Cell 34
PubMed: 19362537 | PubMedCentral: PMC2689388 | DOI: 10.1016/j.molcel.2009.02.026
The ClpB X-ray structure (PDB code:1QVR) was used for docking into the N-terminal density.
Publication Year: 2009
A newly discovered protein export machine in malaria parasites.
(2009) Nature 459
PubMed: 19536257 | PubMedCentral: PMC2725363 | DOI: 10.1038/nature08104
The top two matches, covering Pf HSP101 from residue 35 to the C-terminus, were to Thermus thermophilus ClpB (1QVR) at 38% pairwise sequence identity and to Escherichia coli ClpA (1R6B) at 33%.
The structure of the protein was modelled in MODELLER 40 with 1QVR, chain B, as a template, except in gapped regions and at the C-terminus, where 1R6B was used as a second template.
ATP-driven molecular chaperone machines.
(2013) Biopolymers 99
PubMed: 23877967 | PubMedCentral: PMC3814418 | DOI: 10.1002/bip.22361
Monomer structures of ClpA (a), ClpB (b), and the HslUV chaperone protease complex (c) (PDB ID: 1KSF, 1QVR, and 1KYI).
Publication Year: 2013
Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 24531492 | PubMedCentral: PMC3940203 | DOI: 10.1107/S1399004713030629
Phasing of the ADP-bound wild-type structure was performed by molecular replacement using CNS with residues 520–854 of the full-length ClpB structure (PDB entry 1qvr ; Lee et al. , 2003 %... 6; ) as the search model.
Publication Year: 2014
Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state.
(2014) Sci Rep 4
PubMed: 24658080 | PubMedCentral: PMC3963067 | DOI: 10.1038/srep04442
(B) Homology model of AAA+ modules of mouse mysterin based on a crystal structure of Thermus thermophilus ClpB (PDB ID: 1QVR).
Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation.
(2014) Elife 3
PubMed: 24843029 | PubMedCentral: PMC4023160 | DOI: null
The following previously published datasets were used: Lee S , Sowa ME , Watanabe Y , Sigler PB , Chiu W , Yoshida M and Tsai FTF , 2003 , Crystal Structure Analysis of ClpBmophilus ClpB , http://www.... csb.org/pdb/explore/explore.do?structureId=1QVR , Publicly available at PDB.
Moreover, a very similar intersubunit motif 1-motif 2 contact is seen in all the ClpB crystal structures, in which ClpB monomers are arranged in a spiral assembly ( Tth ClpB, 1QVR, Lee et al., 2003 ; Eco ClpB current study) ( Figure 4—figure supplement 1 ).
PubMed ID is not available.
Published in 2014
Structure of the ClpB chaperone from Thermus thermophilus (1QVR).
trans-Acting arginine residues in the AAA+ chaperone ClpB allosterically regulate the activity through inter- and intradomain communication.
(2014) J Biol Chem 289
PubMed: 25253689 | PubMedCentral: PMC4239642 | DOI: 10.1074/jbc.M114.608828
A , the ClpB construct NBD1-M comprises amino acids 141–534, which are highlighted in dark gray in the crystal structure of full-length ClpB (Protein Data Bank code 1QVR ).
The structural close-up view is based on the available crystal structure of ClpB (Protein Data Bank code 1QVR ) and shows the catalytic site located in the interface between two NBD1 subunits ( green and yellow , respectively) with the conserved, trans -acting arginines Arg-322 and Arg-323 in close proximity to the ATP molecule bound to the neighboring subunit.
The available crystal structure of ClpB from T. thermophilus (Protein Data Bank code 1QVR ) exhibits a helical arrangement of subunits, thereby displaying a shifted subunit interface ( 7 ).
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