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Pectate cleavage
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PDB id
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1air
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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
111:73-92
(1996)
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PubMed id:
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The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.
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S.E.Lietzke,
R.D.Scavetta,
M.D.Yoder,
F.Jurnak.
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ABSTRACT
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The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the
enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics
techniques to a resolution of 2.2 A and an R factor (an agreement factor between
observed structure factor amplitudes) of 16.1%. The final model consists of all
355 amino acids and 157 water molecules. The root-mean-square deviation from
ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The
structure of PelE bound to a lanthanum ion, which inhibits the enzymatic
activity, has also been refined and compared to the metal-free protein. In
addition, the structures of pectate lyase C (PelC) in the presence and absence
of a lutetium ion have been refined further using an improved algorithm for
identifying waters and other solvent molecules. The two putative active site
regions of PelE have been compared to those in the refined structure of PelC.
The analysis of the atomic details of PelE and PelC in the presence and absence
of lanthanide ions provides insight into the enzymatic mechanism of pectate
lyases.
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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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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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Z.Xiao,
H.Bergeron,
S.Grosse,
M.Beauchemin,
M.L.Garron,
D.Shaya,
T.Sulea,
M.Cygler,
and
P.C.Lau
(2008).
Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment.
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Appl Environ Microbiol, 74,
1183-1189.
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PDB codes:
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E.W.Czerwinski,
T.Midoro-Horiuti,
M.A.White,
E.G.Brooks,
and
R.M.Goldblum
(2005).
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
|
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J Biol Chem, 280,
3740-3746.
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PDB code:
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N.Ferguson,
J.Berriman,
M.Petrovich,
T.D.Sharpe,
J.T.Finch,
and
A.R.Fersht
(2003).
Rapid amyloid fiber formation from the fast-folding WW domain FBP28.
|
| |
Proc Natl Acad Sci U S A, 100,
9814-9819.
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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.
|
| |
Acta Crystallogr D Biol Crystallogr, 59,
341-342.
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H.Jing,
J.Takagi,
J.H.Liu,
S.Lindgren,
R.G.Zhang,
A.Joachimiak,
J.H.Wang,
and
T.A.Springer
(2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
|
| |
Structure, 10,
1453-1464.
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PDB code:
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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.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
709-711.
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|
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S.J.Charnock,
I.E.Brown,
J.P.Turkenburg,
G.W.Black,
and
G.J.Davies
(2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
|
| |
Proc Natl Acad Sci U S A, 99,
12067-12072.
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PDB codes:
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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.
|
| |
J Bacteriol, 181,
3705-3709.
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D.W.Bauer,
and
A.Collmer
(1997).
Molecular cloning, characterization, and mutagenesis of a pel gene from Pseudomonas syringae pv. lachyrmans encoding a member of the Erwinia chrysanthemi pelADE family of pectate lyases.
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Mol Plant Microbe Interact, 10,
369-379.
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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
