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PDBsum entry 1grl
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Chaperonin
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Title:
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The crystal structure of the bacterial chaperonin groel at 2.8 angstroms
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Structure:
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Groel (hsp60 class). Chain: a, b, c, d, e, f, g. Engineered: yes. Mutation: yes
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Source:
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Escherichia coli. Organism_taxid: 562. Strain: dh5. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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40mer (from
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Resolution:
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2.80Å
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R-factor:
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0.326
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R-free:
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0.368
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Authors:
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K.Braig,Z.Otwinowski,R.Hegde,D.C.Boisvert,A.Joachimiak,A.L.Horwich, P.B.Sigler
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Key ref:
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K.Braig
et al.
(1994).
The crystal structure of the bacterial chaperonin GroEL at 2.8 A.
Nature,
371,
578-586.
PubMed id:
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Date:
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07-Mar-95
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Release date:
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15-Oct-95
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PROCHECK
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Headers
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References
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P0A6F5
(CH60_ECOLI) -
Chaperonin GroEL from Escherichia coli (strain K12)
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Seq:
Struc:
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548 a.a.
518 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 3 residue positions (black
crosses)
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Enzyme class:
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E.C.5.6.1.7
- chaperonin ATPase.
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Reaction:
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ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
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ATP
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+
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H2O
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+
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folded polypeptide
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=
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ADP
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+
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phosphate
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+
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unfolded polypeptide
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
371:578-586
(1994)
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PubMed id:
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The crystal structure of the bacterial chaperonin GroEL at 2.8 A.
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K.Braig,
Z.Otwinowski,
R.Hegde,
D.C.Boisvert,
A.Joachimiak,
A.L.Horwich,
P.B.Sigler.
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ABSTRACT
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The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14
subunits made of two nearly 7-fold rotationally symmetrical rings stacked
back-to-back with dyad symmetry. The subunits consist of three domains: a large
equatorial domain that forms the foundation of the assembly at its waist and
holds the rings together; a large loosely structured apical domain that forms
the ends of the cylinder; and a small slender intermediate domain that connects
the two, creating side windows. The three-dimensional structure places most of
the mutationally defined functional sites on the channel walls and its outward
invaginations, and at the ends of the cylinder.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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W.A.Hendrickson
(2013).
Evolution of diffraction methods for solving crystal structures.
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Acta Crystallogr A,
69,
51-59.
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F.A.Rey,
and
W.I.Sundquist
(2011).
Macromolecular assemblages.
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Curr Opin Struct Biol,
21,
221-222.
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I.G.Muñoz,
H.Yébenes,
M.Zhou,
P.Mesa,
M.Serna,
A.Y.Park,
E.Bragado-Nilsson,
A.Beloso,
G.de Cárcer,
M.Malumbres,
C.V.Robinson,
J.M.Valpuesta,
and
G.Montoya
(2011).
Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin.
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Nat Struct Mol Biol,
18,
14-19.
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PDB code:
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L.Skjaerven,
A.Martinez,
and
N.Reuter
(2011).
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit.
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Proteins,
79,
232-243.
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A.Albert,
C.Yunta,
R.Arranz,
A.Peña,
E.Salido,
J.M.Valpuesta,
and
J.Martín-Benito
(2010).
Structure of GroEL in complex with an early folding intermediate of alanine glyoxylate aminotransferase.
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J Biol Chem,
285,
6371-6376.
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B.Sielaff,
K.S.Lee,
and
F.T.Tsai
(2010).
Crystallization and preliminary X-ray crystallographic analysis of a GroEL1 fragment from Mycobacterium tuberculosis H37Rv.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
418-420.
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G.A.Frank,
M.Goomanovsky,
A.Davidi,
G.Ziv,
A.Horovitz,
and
G.Haran
(2010).
Out-of-equilibrium conformational cycling of GroEL under saturating ATP concentrations.
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Proc Natl Acad Sci U S A,
107,
6270-6274.
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J.L.England,
and
V.S.Pande
(2010).
Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework.
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Biochem Cell Biol,
88,
359-369.
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J.Zhang,
M.L.Baker,
G.F.Schröder,
N.R.Douglas,
S.Reissmann,
J.Jakana,
M.Dougherty,
C.J.Fu,
M.Levitt,
S.J.Ludtke,
J.Frydman,
and
W.Chiu
(2010).
Mechanism of folding chamber closure in a group II chaperonin.
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Nature,
463,
379-383.
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PDB codes:
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N.R.Voss,
and
M.Gerstein
(2010).
3V: cavity, channel and cleft volume calculator and extractor.
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Nucleic Acids Res,
38,
W555-W562.
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R.Sabate,
N.S.de Groot,
and
S.Ventura
(2010).
Protein folding and aggregation in bacteria.
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Cell Mol Life Sci,
67,
2695-2715.
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T.B.Eronina,
N.A.Chebotareva,
S.G.Bazhina,
S.Y.Kleymenov,
I.N.Naletova,
V.I.Muronetz,
and
B.I.Kurganov
(2010).
Effect of GroEL on thermal aggregation of glycogen phosphorylase b from rabbit skeletal muscle.
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Macromol Biosci,
10,
768-774.
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T.Kanzaki,
S.Ushioku,
A.Nakagawa,
T.Oka,
K.Takahashi,
T.Nakamura,
K.Kuwajima,
A.Yamagishi,
and
M.Yohda
(2010).
Adaptation of a hyperthermophilic group II chaperonin to relatively moderate temperatures.
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Protein Eng Des Sel,
23,
393-402.
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T.Rao,
and
P.A.Lund
(2010).
Differential expression of the multiple chaperonins of Mycobacterium smegmatis.
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FEMS Microbiol Lett,
310,
24-31.
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T.W.Knapman,
V.L.Morton,
N.J.Stonehouse,
P.G.Stockley,
and
A.E.Ashcroft
(2010).
Determining the topology of virus assembly intermediates using ion mobility spectrometry-mass spectrometry.
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Rapid Commun Mass Spectrom,
24,
3033-3042.
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Y.Li,
Z.Zheng,
A.Ramsey,
and
L.Chen
(2010).
Analysis of peptides and proteins in their binding to GroEL.
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J Pept Sci,
16,
693-700.
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A.Korkut,
and
W.A.Hendrickson
(2009).
A force field for virtual atom molecular mechanics of proteins.
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Proc Natl Acad Sci U S A,
106,
15667-15672.
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A.L.Horwich,
and
W.A.Fenton
(2009).
Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding.
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Q Rev Biophys,
42,
83.
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B.Singh,
and
R.S.Gupta
(2009).
Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth.
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Mol Genet Genomics,
281,
361-373.
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C.M.Kumar,
G.Khare,
C.V.Srikanth,
A.K.Tyagi,
A.A.Sardesai,
and
S.C.Mande
(2009).
Facilitated oligomerization of mycobacterial GroEL: evidence for phosphorylation-mediated oligomerization.
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J Bacteriol,
191,
6525-6538.
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C.Weiss,
A.Bonshtien,
O.Farchi-Pisanty,
A.Vitlin,
and
A.Azem
(2009).
Cpn20: Siamese twins of the chaperonin world.
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Plant Mol Biol,
69,
227-238.
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D.K.Clare,
P.J.Bakkes,
H.van Heerikhuizen,
S.M.van der Vies,
and
H.R.Saibil
(2009).
Chaperonin complex with a newly folded protein encapsulated in the folding chamber.
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Nature,
457,
107-110.
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D.Yamamoto,
N.Nagura,
S.Omote,
M.Taniguchi,
and
T.Ando
(2009).
Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy.
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Biophys J,
97,
2358-2367.
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H.M.Lu,
and
J.Liang
(2009).
Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.
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PLoS Comput Biol,
5,
e1000526.
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K.Ayada,
K.Yokota,
K.Kobayashi,
Y.Shoenfeld,
E.Matsuura,
and
K.Oguma
(2009).
Chronic infections and atherosclerosis.
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Clin Rev Allergy Immunol,
37,
44-48.
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O.Kolaj,
S.Spada,
S.Robin,
and
J.G.Wall
(2009).
Use of folding modulators to improve heterologous protein production in Escherichia coli.
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Microb Cell Fact,
8,
9.
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R.F.Khairullin,
A.G.Mikhailova,
T.Y.Sebyakina,
N.L.Lubenets,
R.H.Ziganshin,
I.V.Demidyuk,
T.Y.Gromova,
S.V.Kostrov,
and
L.D.Rumsh
(2009).
Oligopeptidase B from Serratia proteamaculans. I. Determination of primary structure, isolation, and purification of wild-type and recombinant enzyme variants.
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Biochemistry (Mosc),
74,
1164-1172.
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R.Kanno,
A.Koike-Takeshita,
K.Yokoyama,
H.Taguchi,
and
K.Mitsuoka
(2009).
Cryo-EM structure of the native GroEL-GroES complex from thermus thermophilus encapsulating substrate inside the cavity.
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Structure,
17,
287-293.
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T.Nojima,
and
M.Yoshida
(2009).
Probing open conformation of GroEL rings by cross-linking reveals single and double open ring structures of GroEL in ADP and ATP.
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J Biol Chem,
284,
22834-22839.
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V.V.Marchenkov,
and
G.V.Semisotnov
(2009).
GroEL-Assisted Protein Folding: Does It Occur Within the Chaperonin Inner Cavity?
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Int J Mol Sci,
10,
2066-2083.
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Y.Li,
X.Gao,
and
L.Chen
(2009).
GroEL Recognizes an Amphipathic Helix and Binds to the Hydrophobic Side.
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J Biol Chem,
284,
4324-4331.
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A.Koike-Takeshita,
M.Yoshida,
and
H.Taguchi
(2008).
Revisiting the GroEL-GroES Reaction Cycle via the Symmetric Intermediate Implied by Novel Aspects of the GroEL(D398A) Mutant.
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J Biol Chem,
283,
23774-23781.
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C.C.Jolley,
S.A.Wells,
P.Fromme,
and
M.F.Thorpe
(2008).
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.
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Biophys J,
94,
1613-1621.
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C.Dong,
L.Shao,
J.Guo,
and
J.Ren
(2008).
Host-guest interaction of chaperonin GroEL and water-soluble CdTe quantum dots and its size-selective inclusion.
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Chemphyschem,
9,
2245-2251.
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C.L.Lawson,
S.Dutta,
J.D.Westbrook,
K.Henrick,
and
H.M.Berman
(2008).
Representation of viruses in the remediated PDB archive.
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Acta Crystallogr D Biol Crystallogr,
64,
874-882.
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C.R.Booth,
A.S.Meyer,
Y.Cong,
M.Topf,
A.Sali,
S.J.Ludtke,
W.Chiu,
and
J.Frydman
(2008).
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
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Nat Struct Mol Biol,
15,
746-753.
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D.K.Clare,
S.Stagg,
J.Quispe,
G.W.Farr,
A.L.Horwich,
and
H.R.Saibil
(2008).
Multiple states of a nucleotide-bound group 2 chaperonin.
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Structure,
16,
528-534.
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D.Madan,
Z.Lin,
and
H.S.Rye
(2008).
Triggering Protein Folding within the GroEL-GroES Complex.
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J Biol Chem,
283,
32003-32013.
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E.Kurimoto,
Y.Nishi,
Y.Yamaguchi,
T.Zako,
R.Iizuka,
N.Ide,
M.Yohda,
and
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(2008).
Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy.
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Proteins,
70,
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F.M.Codoñer,
S.O'Dea,
and
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(2008).
Reducing the false positive rate in the non-parametric analysis of molecular coevolution.
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BMC Evol Biol,
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G.A.Frank,
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S.S.Daube,
A.Horovitz,
and
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(2008).
Design of an optical switch for studying conformational dynamics in individual molecules of GroEL.
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Bioconjug Chem,
19,
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G.M.Altschuler,
and
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(2008).
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin.
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J R Soc Interface,
5,
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J.Chugh,
S.Sharma,
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and
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(2008).
The structure of CCT-Hsc70 NBD suggests a mechanism for Hsp70 delivery of substrates to the chaperonin.
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Nat Struct Mol Biol,
15,
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(2008).
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| |
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| |
Biophys J,
95,
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| |
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27,
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A.Kono-Okada,
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(2008).
Hydrophilic residues 526 KNDAAD 531 in the flexible C-terminal region of the chaperonin GroEL are critical for substrate protein folding within the central cavity.
|
| |
J Biol Chem,
283,
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M.Kosmaoglou,
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(2008).
Effect of the C-terminal Truncation on the Functional Cycle of Chaperonin GroEL: IMPLICATION THAT THE C-TERMINAL REGION FACILITATES THE TRANSITION FROM THE FOLDING-ARRESTED TO THE FOLDING-COMPETENT STATE.
|
| |
J Biol Chem,
283,
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and
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(2008).
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| |
Mol Microbiol,
69,
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N.Papo,
Y.Kipnis,
G.Haran,
and
A.Horovitz
(2008).
Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET.
|
| |
J Mol Biol,
380,
717-725.
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O.Paliy,
S.M.Gargac,
Y.Cheng,
V.N.Uversky,
and
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(2008).
Protein disorder is positively correlated with gene expression in Escherichia coli.
|
| |
J Proteome Res,
7,
2234-2245.
|
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T.Ando,
T.Uchihashi,
N.Kodera,
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A.Miyagi,
M.Taniguchi,
and
H.Yamashita
(2008).
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|
| |
Pflugers Arch,
456,
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T.Furuta,
Y.Fujitsuka,
G.Chikenji,
and
S.Takada
(2008).
In silico chaperonin-like cycle helps folding of proteins for structure prediction.
|
| |
Biophys J,
94,
2558-2565.
|
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|
|
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|
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T.Inobe,
K.Takahashi,
K.Maki,
S.Enoki,
K.Kamagata,
A.Kadooka,
M.Arai,
and
K.Kuwajima
(2008).
Asymmetry of the GroEL-GroES complex under physiological conditions as revealed by small-angle x-ray scattering.
|
| |
Biophys J,
94,
1392-1402.
|
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T.Nojima,
S.Murayama,
M.Yoshida,
and
F.Motojima
(2008).
Determination of the number of active GroES subunits in the fused heptamer GroES required for interactions with GroEL.
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PDB code:
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PDB code:
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Identification of GroEL as a constituent of an mRNA-protection complex in Escherichia coli.
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J Biol Chem,
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Cell,
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Inactive GroEL monomers can be isolated and reassembled to functional tetradecamers that contain few bound peptides.
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Refolding and reassembly of active chaperonin GroEL after denaturation.
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J Biol Chem,
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Nat Struct Biol,
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PDB code:
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Kinetic analysis of interactions between GroEL and reduced alpha-lactalbumin. Effect of GroES and nucleotides.
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J Biol Chem,
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A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
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PDB codes:
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PDB code:
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A monomeric variant of GroEL binds nucleotides but is inactive as a molecular chaperone.
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G.H.Lorimer
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How chaperones tell wrong from right.
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| |
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| |
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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|
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