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* Residue conservation analysis
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Enzyme class:
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E.C.4.2.2.2
- Pectate lyase.
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Pathway:
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Pectin and Pectate Lyases
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Reaction:
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Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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1 term
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Biological process
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pathogenesis
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1 term
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Biochemical function
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lyase activity
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3 terms
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Plant Physiol
107:349-364
(1995)
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PubMed id:
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The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
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M.D.Yoder,
F.Jurnak.
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ABSTRACT
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The crystal structure of pectate lyase C (EC 4.2.2.2) from the enterobacterium
Erwinia chrysanthemi (PelC) has been refined by molecular dynamics techniques to
a resolution of 2.2 A to an R factor of 17.97%. The final model consists of 352
of the total 353 amino acids and 114 solvent molecules. The root-mean-square
deviation from ideality is 0.009 A for bond lengths and 1.768[deg] for bond
angles. The structure of PelC bound to the lanthanide ion lutetium, used as a
calcium analog, has also been refined. Lutetium inhibits the enzymatic activity
of the protein, and in the PelC-lutetium structure, the ion binds in the
putative calcium-binding site. Five side-chain atoms form ligands to the
lutetium ion. An analysis of the atomic-level model of the two protein
structures reveals possible implications for the enzymatic mechanism of the
enzyme.
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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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A.K.Dubey,
S.Yadav,
M.Kumar,
V.K.Singh,
B.K.Sarangi,
and
D.Yadav
(2010).
In silico characterization of pectate lyase protein sequences from different source organisms.
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Enzyme Res, 2010,
950230.
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A.Ochiai,
T.Itoh,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2009).
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases.
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J Biol Chem, 284,
10181-10189.
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PDB codes:
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D.W.Abbott,
and
A.B.Boraston
(2008).
Structural biology of pectin degradation by Enterobacteriaceae.
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Microbiol Mol Biol Rev, 72,
301.
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C.H.Liao,
W.Fett,
S.S.Tzean,
and
G.Hoffman
(2006).
Detection and sequence analysis of an altered pectate lyase gene in Pseudomonas syringae pv. glycinea and related bacteria.
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Can J Microbiol, 52,
1051-1059.
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C.S.Rye,
A.Matte,
M.Cygler,
and
S.G.Withers
(2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
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Chembiochem, 7,
631-637.
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S.A.Douthit,
M.Dlakic,
D.E.Ohman,
and
M.J.Franklin
(2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
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J Bacteriol, 187,
4573-4583.
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T.Nakaniwa,
T.Tada,
K.Ishii,
M.Takao,
T.Sakai,
and
K.Nishimura
(2003).
Crystallization and preliminary X-ray analysis of a thermostable pectate lyase PL 47 from Bacillus sp. TS 47.
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Acta Crystallogr D Biol Crystallogr, 59,
341-342.
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L.Cowen,
P.Bradley,
M.Menke,
J.King,
and
B.Berger
(2002).
Predicting the beta-helix fold from protein sequence data.
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J Comput Biol, 9,
261-276.
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M.A.McDonough,
C.Ryttersgaard,
M.E.Bjørnvad,
L.Lo Leggio,
M.Schülein,
S.O.Schrøder Glad,
and
S.Larsen
(2002).
Crystallization and preliminary X-ray characterization of a thermostable pectate lyase from Thermotoga maritima.
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Acta Crystallogr D Biol Crystallogr, 58,
709-711.
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Y.Iwamoto,
R.Araki,
K.Iriyama,
T.Oda,
H.Fukuda,
S.Hayashida,
and
T.Muramatsu
(2001).
Purification and characterization of bifunctional alginate lyase from Alteromonas sp. strain no. 272 and its action on saturated oligomeric substrates.
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Biosci Biotechnol Biochem, 65,
133-142.
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M.Takao,
T.Nakaniwa,
K.Yoshikawa,
T.Terashita,
and
T.Sakai
(2000).
Purification and characterization of thermostable pectate lyase with protopectinase activity from thermophilic Bacillus sp. TS 47.
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Biosci Biotechnol Biochem, 64,
2360-2367.
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Y.Hatada,
K.Saito,
K.Koike,
T.Yoshimatsu,
T.Ozawa,
T.Kobayashi,
and
S.Ito
(2000).
Deduced amino-acid sequence and possible catalytic residues of a novel pectate lyase from an alkaliphilic strain of Bacillus.
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Eur J Biochem, 267,
2268-2275.
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C.Roy,
H.Kester,
J.Visser,
V.Shevchik,
N.Hugouvieux-Cotte-Pattat,
J.Robert-Baudouy,
and
J.Benen
(1999).
Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937.
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J Bacteriol, 181,
3705-3709.
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W.Grabarse,
M.Vaupel,
J.A.Vorholt,
S.Shima,
R.K.Thauer,
A.Wittershagen,
G.Bourenkov,
H.D.Bartunik,
and
U.Ermler
(1999).
The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri.
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Structure, 7,
1257-1268.
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PDB code:
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Y.Hatada,
N.Higaki,
K.Saito,
A.Ogawa,
K.Sawada,
T.Ozawa,
Y.Hakamada,
T.Kobayashi,
and
S.Ito
(1999).
Cloning and sequencing of a high-alkaline pectate lyase gene from an alkaliphilic Bacillus isolate.
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Biosci Biotechnol Biochem, 63,
998.
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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
codes are
shown on the right.
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Links
