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PDBsum entry 1gec
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Hydrolase/hydrolase inhibitor
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PDB id
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1gec
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.22.25
- glycyl endopeptidase.
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Reaction:
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Preferential cleavage: Gly-|-Xaa, in proteins and in small molecule substrates.
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DOI no:
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Biochemistry
34:13190-13195
(1995)
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PubMed id:
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Crystal structure of glycyl endopeptidase from Carica papaya: a cysteine endopeptidase of unusual substrate specificity.
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B.P.O'Hara,
A.M.Hemmings,
D.J.Buttle,
L.H.Pearl.
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ABSTRACT
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Glycyl endopeptidase is a cysteine endopeptidase of the papain family,
characterized by specificity for cleavage C-terminal to glycyl residues only and
by resistance to inhibition by members of the cystatin family of cysteine
proteinase inhibitors. Glycyl endopeptidase has been crystallized from high salt
with a substrate-like inhibitor covalently bound to the catalytic Cys 25. The
structure has been solved by molecular replacement with the structure of papain
and refined at 2.1 A to an R factor of 0.196 (Rfree = 0.258) with good geometry.
The structure of the S1 substrate binding site of glycyl endopeptidase differs
from that of papain by the substitution of glycines at residues 23 and 65 in
papain, with glutamic acid and arginine, respectively, in glycyl endopeptidase.
The side chains of these residues form a barrier across the binding pocket,
effectively excluding substrate residues with large side chains from the S1
subsite. The constriction of this subsite in glycyl endopeptidase explains the
unique specificity of this enzyme for cleavage after glycyl residues and is a
major component of its resistance to inhibition by cystatins.
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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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S.Ishii,
T.Yano,
and
H.Hayashi
(2006).
Expression and characterization of the peptidase domain of Streptococcus pneumoniae ComA, a bifunctional ATP-binding cassette transporter involved in quorum sensing pathway.
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J Biol Chem,
281,
4726-4731.
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M.C.Oliver-Salvador,
L.A.González-Ramírez,
J.A.Gavira,
M.Soriano-García,
and
J.M.García-Ruiz
(2004).
Purification, crystallization and preliminary X-ray analysis of mexicain.
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Acta Crystallogr D Biol Crystallogr,
60,
2058-2060.
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M.Zhu,
F.Shao,
R.W.Innes,
J.E.Dixon,
and
Z.Xu
(2004).
The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.
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Proc Natl Acad Sci U S A,
101,
302-307.
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PDB code:
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A.Nayeem,
S.Krystek,
and
T.Stouch
(2003).
An assessment of protein-ligand binding site polarizability.
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Biopolymers,
70,
201-211.
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K.Ito,
X.Ma,
N.Azmi,
H.S.Huang,
M.Fujii,
and
T.Yoshimoto
(2003).
Novel aminopeptidase specific for glycine from Actinomucor elegans.
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Biosci Biotechnol Biochem,
67,
83-88.
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N.D.Rawlings,
and
A.J.Barrett
(2000).
MEROPS: the peptidase database.
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Nucleic Acids Res,
28,
323-325.
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C.Czaplewski,
Z.Grzonka,
M.Jaskólski,
F.Kasprzykowski,
M.Kozak,
E.Politowska,
and
J.Ciarkowski
(1999).
Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
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Biochim Biophys Acta,
1431,
290-305.
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J.Herold,
S.G.Siddell,
and
A.E.Gorbalenya
(1999).
A human RNA viral cysteine proteinase that depends upon a unique Zn2+-binding finger connecting the two domains of a papain-like fold .
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J Biol Chem,
274,
14918-14925.
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M.E.McGrath
(1999).
The lysosomal cysteine proteases.
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Annu Rev Biophys Biomol Struct,
28,
181-204.
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D.Turk,
G.Guncar,
M.Podobnik,
and
B.Turk
(1998).
Revised definition of substrate binding sites of papain-like cysteine proteases.
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Biol Chem,
379,
137-147.
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S.C.Johnston,
C.N.Larsen,
W.J.Cook,
K.D.Wilkinson,
and
C.P.Hill
(1997).
Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution.
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EMBO J,
16,
3787-3796.
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PDB code:
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W.Baumeister,
Z.Cejka,
M.Kania,
and
E.Seemüller
(1997).
The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.
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Biol Chem,
378,
121-130.
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D.Maes,
J.Bouckaert,
F.Poortmans,
L.Wyns,
and
Y.Looze
(1996).
Structure of chymopapain at 1.7 A resolution.
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Biochemistry,
35,
16292-16298.
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PDB code:
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M.R.Groves,
M.A.Taylor,
M.Scott,
N.J.Cummings,
R.W.Pickersgill,
and
J.A.Jenkins
(1996).
The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft.
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Structure,
4,
1193-1203.
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PDB code:
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N.A.Katerelos,
and
P.W.Goodenough
(1996).
Rapid kinetic studies and structural determination of a cysteine proteinase mutant imply that residue 158 in caricain has a major effect upon the ability of the active site histidine to protonate a dipyridyl probe.
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Biochemistry,
35,
14763-14772.
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R.Coulombe,
P.Grochulski,
J.Sivaraman,
R.Ménard,
J.S.Mort,
and
M.Cygler
(1996).
Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment.
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EMBO J,
15,
5492-5503.
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PDB code:
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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
