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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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Biochemical function
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lyase activity
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3 terms
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DOI no:
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Acta Crystallogr D Biol Crystallogr
58:1008-1015
(2002)
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PubMed id:
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Structure of pectate lyase A: comparison to other isoforms.
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L.M.Thomas,
C.N.Doan,
R.L.Oliver,
M.D.Yoder.
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ABSTRACT
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Pectate lyase A is a virulence factor secreted by the plant-pathogenic bacteria
Erwinia chrysanthemi. The enzyme cleaves the glycosidic bond of pectate polymers
by a calcium-dependent beta-elimination mechanism. The crystal structure of
pectate lyase A from E. chrysanthemi EC16 has been determined in two crystal
forms, monoclinic C2 to 1.8 A and rhombohedral R3 to 2.1 A. The protein
structure is compared with two other pectate lyase isoforms from E. chrysanthemi
EC16, pectate lyase C and pectate lyase E. Pectate lyase A is unique as it is
the only acidic pectate lyase and has end products that are significantly more
varied in length in comparison to those of the other four major pectate lyase
isozymes. Differences and similarities in polypeptide trace, size and volume of
the active-site groove and surface electrostatics are discussed.
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Selected figure(s)
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Figure 2.
Figure 2 Structure of PelA from E. chrysanthemi. (a) A
ribbons-style representation with the three parallel  -sheets
of the parallel -helix
shown in different colors: yellow for PB1, blue for PB2 and red
for PB3. The two -ribbons
not participating in the parallel -helix
are shown in green. The disulfide bond is drawn as an orange
thunderbolt. The N- and C-termini are labeled `N' and `C',
respectively. (b) Stereo diagram of the C^  chain
trace of PelA in the C2 crystal form. Residue numbers throughout
the molecule are indicated.
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Figure 5.
Figure 5 Active-site groove of PelA, PelC and PelE. The masked
active-site groove is displayed in cyan, with the C^ chain
trace of the proteins in red. (a) PelA, (b) PelC, (c) PelE.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2002,
58,
1008-1015)
copyright 2002.
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Figures were
selected
by an automated process.
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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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K.L.Hindle,
J.Bella,
and
S.C.Lovell
(2009).
Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.
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Proteins, 77,
342-358.
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C.Creze,
S.Castang,
E.Derivery,
R.Haser,
N.Hugouvieux-Cotte-Pattat,
V.E.Shevchik,
and
P.Gouet
(2008).
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.
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J Biol Chem, 283,
18260-18268.
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PDB codes:
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A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2007).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.
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J Biol Chem, 282,
37134-37145.
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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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E.F.Pettersen,
T.D.Goddard,
C.C.Huang,
G.S.Couch,
D.M.Greenblatt,
E.C.Meng,
and
T.E.Ferrin
(2004).
UCSF Chimera--a visualization system for exploratory research and analysis.
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J Comput Chem, 25,
1605-1612.
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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
