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PDBsum entry 1cpm
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Hydrolase(glucanase)
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PDB id
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1cpm
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.73
- licheninase.
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Reaction:
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Hydrolysis of 1,4-beta-D-glycosidic linkages in beta-D-glucans containing 1,3- and 1,4-bonds.
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DOI no:
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Proc Natl Acad Sci U S A
91:10417-10421
(1994)
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PubMed id:
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Native-like in vivo folding of a circularly permuted jellyroll protein shown by crystal structure analysis.
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M.Hahn,
K.Piotukh,
R.Borriss,
U.Heinemann.
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ABSTRACT
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A jellyroll beta-sandwich protein, the Bacillus beta-glucanase H(A16-M), is used
to probe the role of N-terminal peptide regions in protein folding in vivo. A
gene encoding H(A16-M) is rearranged to place residues 1-58 of the protein
behind a signal peptide and residues 59-214. The rearranged gene is expressed in
Escherichia coli. The resultant circularly permuted protein, cpA16M-59, is
secreted into the periplasm, correctly processed, and folded into a stable and
active enzyme. Crystal structure analysis at 2.0-A resolution, R = 15.3%, shows
cpA16M-59 to have a three-dimensional structure nearly identical with that of
the parent beta-glucanase. An analogous experiment based on the wild-type
Bacillus macerans beta-glucanase, giving rise to the circularly permuted variant
cpMAC-57, yields the same results. Folding of these proteins, therefore, is not
a vectorial process depending on the conformation adopted by their native
N-terminal oligopeptides after ribosomal synthesis and translocation through the
cytoplasmic membrane.
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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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Y.Yu,
and
S.Lutz
(2011).
Circular permutation: a different way to engineer enzyme structure and function.
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Trends Biotechnol,
29,
18-25.
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T.Schmidt-Goenner,
A.Guerler,
B.Kolbeck,
and
E.W.Knapp
(2010).
Circular permuted proteins in the universe of protein folds.
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Proteins,
78,
1618-1630.
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C.S.Crowley,
M.R.Sawaya,
T.A.Bobik,
and
T.O.Yeates
(2008).
Structure of the PduU shell protein from the Pdu microcompartment of Salmonella.
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Structure,
16,
1324-1332.
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PDB code:
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G.Fibriansah,
S.Masuda,
N.Koizumi,
S.Nakamura,
and
T.Kumasaka
(2007).
The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
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Proteins,
69,
683-690.
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PDB code:
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Z.Qian,
C.J.Fields,
and
S.Lutz
(2007).
Investigating the structural and functional consequences of circular permutation on lipase B from Candida antarctica.
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Chembiochem,
8,
1989-1996.
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T.Hohm,
P.Limbourg,
and
D.Hoffmann
(2006).
A multiobjective evolutionary method for the design of peptidic mimotopes.
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J Comput Biol,
13,
113-125.
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M.Kojima,
K.Ayabe,
and
H.Ueda
(2005).
Importance of terminal residues on circularly permutated Escherichia coli alkaline phosphatase with high specific activity.
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J Biosci Bioeng,
100,
197-202.
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B.A.Manjasetty,
J.Hennecke,
R.Glockshuber,
and
U.Heinemann
(2004).
Structure of circularly permuted DsbA(Q100T99): preserved global fold and local structural adjustments.
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Acta Crystallogr D Biol Crystallogr,
60,
304-309.
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PDB code:
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T.U.Schwartz,
R.Walczak,
and
G.Blobel
(2004).
Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit.
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Protein Sci,
13,
2814-2818.
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P.Tougard,
T.Bizebard,
M.Ritco-Vonsovici,
P.Minard,
and
M.Desmadril
(2002).
Structure of a circularly permuted phosphoglycerate kinase.
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Acta Crystallogr D Biol Crystallogr,
58,
2018-2023.
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PDB code:
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L.C.Tsai,
L.F.Shyur,
S.S.Lin,
and
H.S.Yuan
(2001).
Crystallization and preliminary X-ray diffraction analysis of the 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes.
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Acta Crystallogr D Biol Crystallogr,
57,
1303-1306.
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P.T.Beernink,
Y.R.Yang,
R.Graf,
D.S.King,
S.S.Shah,
and
H.K.Schachman
(2001).
Random circular permutation leading to chain disruption within and near alpha helices in the catalytic chains of aspartate transcarbamoylase: effects on assembly, stability, and function.
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Protein Sci,
10,
528-537.
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X.Ni,
and
H.K.Schachman
(2001).
In vivo assembly of aspartate transcarbamoylase from fragmented and circularly permuted catalytic polypeptide chains.
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Protein Sci,
10,
519-527.
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A.Planas
(2000).
Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering.
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Biochim Biophys Acta,
1543,
361-382.
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C.A.McWherter,
Y.Feng,
L.L.Zurfluh,
B.K.Klein,
M.P.Baganoff,
J.O.Polazzi,
W.F.Hood,
K.Paik,
A.L.Abegg,
E.S.Grabbe,
J.J.Shieh,
A.M.Donnelly,
and
J.P.McKearn
(1999).
Circular permutation of the granulocyte colony-stimulating factor receptor agonist domain of myelopoietin.
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Biochemistry,
38,
4564-4571.
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Y.Feng,
J.C.Minnerly,
L.L.Zurfluh,
W.D.Joy,
W.F.Hood,
A.L.Abegg,
E.S.Grabbe,
J.J.Shieh,
T.L.Thurman,
J.P.McKearn,
and
C.A.McWherter
(1999).
Circular permutation of granulocyte colony-stimulating factor.
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Biochemistry,
38,
4553-4563.
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D.E.Otzen,
and
A.R.Fersht
(1998).
Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus.
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Biochemistry,
37,
8139-8146.
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J.Aÿ,
F.Götz,
R.Borriss,
and
U.Heinemann
(1998).
Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain.
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Proc Natl Acad Sci U S A,
95,
6613-6618.
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PDB code:
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J.Aÿ,
M.Hahn,
K.Decanniere,
K.Piotukh,
R.Borriss,
and
U.Heinemann
(1998).
Crystal structures and properties of de novo circularly permuted 1,3-1,4-beta-glucanases.
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Proteins,
30,
155-167.
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PDB codes:
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M.Iwakura
(1998).
In search of circular permuted variants of Escherichia coli dihydrofolate reductase.
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Biosci Biotechnol Biochem,
62,
778-781.
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V.Chu,
S.Freitag,
I.Le Trong,
R.E.Stenkamp,
and
P.S.Stayton
(1998).
Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.
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Protein Sci,
7,
848-859.
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PDB codes:
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U.Pieper,
K.Hayakawa,
Z.Li,
and
O.Herzberg
(1997).
Circularly permuted beta-lactamase from Staphylococcus aureus PC1.
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Biochemistry,
36,
8767-8774.
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PDB code:
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W.Gong,
M.O'Gara,
R.M.Blumenthal,
and
X.Cheng
(1997).
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
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Nucleic Acids Res,
25,
2702-2715.
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PDB code:
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Y.Lindqvist,
and
G.Schneider
(1997).
Circular permutations of natural protein sequences: structural evidence.
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Curr Opin Struct Biol,
7,
422-427.
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P.Zhang,
and
H.K.Schachman
(1996).
In vivo formation of allosteric aspartate transcarbamoylase containing circularly permuted catalytic polypeptide chains: implications for protein folding and assembly.
|
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Protein Sci,
5,
1290-1300.
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R.Graf,
and
H.K.Schachman
(1996).
Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase.
|
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Proc Natl Acad Sci U S A,
93,
11591-11596.
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K.Welfle,
R.Misselwitz,
H.Welfle,
O.Politz,
and
R.Borriss
(1995).
Influence of Ca2+ on conformation and stability of three bacterial hybrid glucanases.
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Eur J Biochem,
229,
726-735.
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M.Hahn,
T.Keitel,
and
U.Heinemann
(1995).
Crystal and molecular structure at 0.16-nm resolution of the hybrid Bacillus endo-1,3-1,4-beta-D-glucan 4-glucanohydrolase H(A16-M).
|
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Eur J Biochem,
232,
849-858.
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PDB code:
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M.L.Vignais,
C.Corbier,
G.Mulliert,
C.Branlant,
and
G.Branlant
(1995).
Circular permutation within the coenzyme binding domain of the tetrameric glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.
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Protein Sci,
4,
994.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
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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Links
