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PDBsum entry 1pcl
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Lyase (acting on polysaccharides)
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PDB id
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1pcl
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Contents |
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* Residue conservation analysis
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* C-alpha coords only
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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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DOI no:
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Structure
1:241-251
(1993)
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PubMed id:
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Unusual structural features in the parallel beta-helix in pectate lyases.
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M.D.Yoder,
S.E.Lietzke,
F.Jurnak.
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ABSTRACT
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BACKGROUND: A new type of domain structure, an all parallel beta class, has
recently been observed in two pectate lyases, PelC and PelE. The atomic models
have been analyzed to determine whether the new tertiary fold exhibits unusual
structural features. RESULTS: The polypeptide backbone exhibits no new types of
secondary structural elements. However, novel features occur in the amino acid
side chain interactions. The side chain atoms form linear stacks that include
asparagine ladders, serine stacks, aliphatic stacks, and ringed-residue stacks.
A new type of beta-sandwich between parallel beta-sheets is observed with
properties that are more characteristic of antiparallel beta-sheets. CONCLUSION:
An analysis of the PelC and PelE structures, belonging to an all parallel beta
structural class, reveals novel amino acid side chain interactions, a new type
of beta-sandwich and an atypical amino acid composition of parallel beta-sheets.
The findings are relevant to three-dimensional structural predictions.
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Selected figure(s)
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Figure 1.
Fig. 1. Schematics of PelC and PelE. Ribbon iagram of (a) PelC and (b) PelE. Arrows represent ~-structure, and coils represent e~-helices.
Each of the three parallel sheets is depicted in a different color, PB2 is ingree, PB1 in yelow and PB3 in red. (c) The superposition of
the core regions f PelE on PelC. Loops extending out from the core region are xcluded. Th PeIC C~ chain trace is in yellow and the
PelE Cc~ chain trace is in blue.
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Figure 7.
Fig. 7. The hydrogen bonding pattern
of the asparagine ladder. Three
aspargine residues of the asparagine
ladder in PeIC. (b) Three residues of
the asparagine ladder in PelE, includ'-
ing Ser307. The Cc~ chain trace is in
gray. Carbon atoms are lack; itrogen
atoms, dark ray; oxygen atoms, gray;
and hydrogen atoms, white. Hydrogen
bons are indicated by dashed lines.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1993,
1,
241-251)
copyright 1993.
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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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J.Jorda,
B.Xue,
V.N.Uversky,
and
A.V.Kajava
(2010).
Protein tandem repeats - the more perfect, the less structured.
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FEBS J,
277,
2673-2682.
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P.Firozi,
W.Zhang,
L.Chen,
F.A.Quiocho,
K.C.Worley,
and
N.S.Templeton
(2010).
Identification and removal of colanic acid from plasmid DNA preparations: implications for gene therapy.
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Gene Ther,
17,
1484-1499.
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Y.Lei,
Y.Z.Liu,
W.F.Zeng,
and
X.X.Deng
(2010).
Physicochemical and molecular analysis of cell wall metabolism between two navel oranges (Citrus sinensis) with different mastication traits.
|
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J Sci Food Agric,
90,
1479-1484.
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T.Ishida,
S.Fushinobu,
R.Kawai,
M.Kitaoka,
K.Igarashi,
and
M.Samejima
(2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
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J Biol Chem,
284,
10100-10109.
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PDB codes:
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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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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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J.J.Müller,
S.Barbirz,
K.Heinle,
A.Freiberg,
R.Seckler,
and
U.Heinemann
(2008).
An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.
|
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Structure,
16,
766-775.
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PDB codes:
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Q.R.Fan,
and
W.A.Hendrickson
(2008).
Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.
|
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Proteins,
72,
393-401.
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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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D.W.Abbott,
and
A.B.Boraston
(2007).
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.
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J Biol Chem,
282,
35328-35336.
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PDB codes:
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T.J.Oldfield
(2007).
CAALIGN: a program for pairwise and multiple protein-structure alignment.
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Acta Crystallogr D Biol Crystallogr,
63,
514-525.
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A.V.McDonnell,
M.Menke,
N.Palmer,
J.King,
L.Cowen,
and
B.Berger
(2006).
Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins.
|
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Proteins,
63,
976-985.
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M.Margittai,
and
R.Langen
(2006).
Side chain-dependent stacking modulates tau filament structure.
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J Biol Chem,
281,
37820-37827.
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P.Iengar,
N.V.Joshi,
and
P.Balaram
(2006).
Conformational and sequence signatures in beta helix proteins.
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Structure,
14,
529-542.
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R.Stern,
and
M.J.Jedrzejas
(2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
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Chem Rev,
106,
818-839.
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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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J.C.Chan,
N.A.Oyler,
W.M.Yau,
and
R.Tycko
(2005).
Parallel beta-sheets and polar zippers in amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p.
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Biochemistry,
44,
10669-10680.
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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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G.Michel,
K.Pojasek,
Y.Li,
T.Sulea,
R.J.Linhardt,
R.Raman,
V.Prabhakar,
R.Sasisekharan,
and
M.Cygler
(2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
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J Biol Chem,
279,
32882-32896.
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PDB codes:
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H.Novoa De Armas,
C.Verboven,
C.De Ranter,
J.Desair,
A.Vande Broek,
J.Vanderleyden,
and
A.Rabijns
(2004).
Azospirillum irakense pectate lyase displays a toroidal fold.
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Acta Crystallogr D Biol Crystallogr,
60,
999.
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PDB code:
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A.Freiberg,
R.Morona,
L.Van den Bosch,
C.Jung,
J.Behlke,
N.Carlin,
R.Seckler,
and
U.Baxa
(2003).
The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the beta-helix domain.
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J Biol Chem,
278,
1542-1548.
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A.M.Larsson,
R.Andersson,
J.Ståhlberg,
L.Kenne,
and
T.A.Jones
(2003).
Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.
|
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Structure,
11,
1111-1121.
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PDB codes:
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D.Liu,
T.Midoro-Horiuti,
M.A.White,
E.G.Brooks,
R.M.Goldblum,
and
E.W.Czerwinski
(2003).
Crystallization and preliminary X-ray diffraction analysis of Jun a 1, the major allergen isolated from pollen of the mountain cedar Juniperus ashei.
|
| |
Acta Crystallogr D Biol Crystallogr,
59,
1052-1054.
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|
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S.J.Dehdashti,
C.N.Doan,
K.L.Chao,
and
M.D.Yoder
(2003).
Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16.
|
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Acta Crystallogr D Biol Crystallogr,
59,
1339-1342.
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PDB codes:
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W.Hashimoto,
H.Nankai,
B.Mikami,
and
K.Murata
(2003).
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
|
| |
J Biol Chem,
278,
7663-7673.
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PDB codes:
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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.
|
| |
J Comput Biol,
9,
261-276.
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L.M.Thomas,
C.N.Doan,
R.L.Oliver,
and
M.D.Yoder
(2002).
Structure of pectate lyase A: comparison to other isoforms.
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Acta Crystallogr D Biol Crystallogr,
58,
1008-1015.
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PDB codes:
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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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C.W.Ward,
and
T.P.Garrett
(2001).
The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules.
|
| |
BMC Bioinformatics,
2,
4.
|
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G.Michel,
L.Chantalat,
E.Fanchon,
B.Henrissat,
B.Kloareg,
and
O.Dideberg
(2001).
The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide.
|
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J Biol Chem,
276,
40202-40209.
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PDB code:
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M.Akita,
A.Suzuki,
T.Kobayashi,
S.Ito,
and
T.Yamane
(2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
|
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Acta Crystallogr D Biol Crystallogr,
57,
1786-1792.
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PDB code:
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P.Bradley,
L.Cowen,
M.Menke,
J.King,
and
B.Berger
(2001).
BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.
|
| |
Proc Natl Acad Sci U S A,
98,
14819-14824.
|
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S.P.Graether,
and
Z.Jia
(2001).
Modeling Pseudomonas syringae ice-nucleation protein as a beta-helical protein.
|
| |
Biophys J,
80,
1169-1173.
|
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|
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L.C.Serpell
(2000).
Alzheimer's amyloid fibrils: structure and assembly.
|
| |
Biochim Biophys Acta,
1502,
16-30.
|
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M.Akita,
A.Suzuki,
T.Kobayashi,
S.Ito,
and
T.Yamane
(2000).
Crystallization and preliminary X-ray analysis of high-alkaline pectate lyase.
|
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Acta Crystallogr D Biol Crystallogr,
56,
749-750.
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PDB code:
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S.R.Herron,
J.A.Benen,
R.D.Scavetta,
J.Visser,
and
F.Jurnak
(2000).
Structure and function of pectic enzymes: virulence factors of plant pathogens.
|
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Proc Natl Acad Sci U S A,
97,
8762-8769.
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T.Y.Wong,
L.A.Preston,
and
N.L.Schiller
(2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
|
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Annu Rev Microbiol,
54,
289-340.
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K.Brown,
F.Pompeo,
S.Dixon,
D.Mengin-Lecreulx,
C.Cambillau,
and
Y.Bourne
(1999).
Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
|
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EMBO J,
18,
4096-4107.
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PDB codes:
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M.A.Bekri,
J.Desair,
V.Keijers,
P.Proost,
M.Searle-van Leeuwen,
J.Vanderleyden,
and
A.Vande Broek
(1999).
Azospirillum irakense produces a novel type of pectate lyase.
|
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J Bacteriol,
181,
2440-2447.
|
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|
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C.A.Orengo,
A.M.Martin,
G.Hutchinson,
S.Jones,
D.T.Jones,
A.D.Michie,
M.B.Swindells,
and
J.M.Thornton
(1998).
Classifying a protein in the CATH database of domain structures.
|
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Acta Crystallogr D Biol Crystallogr,
54,
1155-1167.
|
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|
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C.Finnie,
A.Zorreguieta,
N.M.Hartley,
and
J.A.Downie
(1998).
Characterization of Rhizobium leguminosarum exopolysaccharide glycanases that are secreted via a type I exporter and have a novel heptapeptide repeat motif.
|
| |
J Bacteriol,
180,
1691-1699.
|
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|
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D.D.Busath,
C.D.Thulin,
R.W.Hendershot,
L.R.Phillips,
P.Maughan,
C.D.Cole,
N.C.Bingham,
S.Morrison,
L.C.Baird,
R.J.Hendershot,
M.Cotten,
and
T.A.Cross
(1998).
Noncontact dipole effects on channel permeation. I. Experiments with (5F-indole)Trp13 gramicidin A channels.
|
| |
Biophys J,
75,
2830-2844.
|
|
|
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C.Chothia,
T.Hubbard,
S.Brenner,
H.Barns,
and
A.Murzin
(1997).
Protein folds in the all-beta and all-alpha classes.
|
| |
Annu Rev Biophys Biomol Struct,
26,
597-627.
|
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|
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E.Domann,
S.Zechel,
A.Lingnau,
T.Hain,
A.Darji,
T.Nichterlein,
J.Wehland,
and
T.Chakraborty
(1997).
Identification and characterization of a novel PrfA-regulated gene in Listeria monocytogenes whose product, IrpA, is highly homologous to internalin proteins, which contain leucine-rich repeats.
|
| |
Infect Immun,
65,
101-109.
|
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F.Tardy,
W.Nasser,
J.Robert-Baudouy,
and
N.Hugouvieux-Cotte-Pattat
(1997).
Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: enzyme characteristics and potential inhibitors.
|
| |
J Bacteriol,
179,
2503-2511.
|
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|
|
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|
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V.E.Shevchik,
J.Robert-Baudouy,
and
N.Hugouvieux-Cotte-Pattat
(1997).
Pectate lyase PelI of Erwinia chrysanthemi 3937 belongs to a new family.
|
| |
J Bacteriol,
179,
7321-7330.
|
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|
|
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|
|
B.Kobe
(1996).
Leucines on a roll.
|
| |
Nat Struct Biol,
3,
977-980.
|
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|
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|
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C.Blake,
and
L.Serpell
(1996).
Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous beta-sheet helix.
|
| |
Structure,
4,
989-998.
|
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|
|
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N.Kita,
C.M.Boyd,
M.R.Garrett,
F.Jurnak,
and
N.T.Keen
(1996).
Differential effect of site-directed mutations in pelC on pectate lyase activity, plant tissue maceration, and elicitor activity.
|
| |
J Biol Chem,
271,
26529-26535.
|
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|
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R.Sasisekharan,
G.Venkataraman,
R.Godavarti,
S.Ernst,
C.L.Cooney,
and
R.Langer
(1996).
Heparinase I from Flavobacterium heparinum. Mapping and characterization of the heparin binding domain.
|
| |
J Biol Chem,
271,
3124-3131.
|
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|
|
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|
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B.Kobe,
and
J.Deisenhofer
(1995).
Proteins with leucine-rich repeats.
|
| |
Curr Opin Struct Biol,
5,
409-416.
|
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|
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E.Lojkowska,
C.Masclaux,
M.Boccara,
J.Robert-Baudouy,
and
N.Hugouvieux-Cotte-Pattat
(1995).
Characterization of the pelL gene encoding a novel pectate lyase of Erwinia chrysanthemi 3937.
|
| |
Mol Microbiol,
16,
1183-1195.
|
|
|
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|
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S.Ernst,
R.Langer,
C.L.Cooney,
and
R.Sasisekharan
(1995).
Enzymatic degradation of glycosaminoglycans.
|
| |
Crit Rev Biochem Mol Biol,
30,
387-444.
|
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|
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T.E.Benson,
D.J.Filman,
C.T.Walsh,
and
J.M.Hogle
(1995).
An enzyme-substrate complex involved in bacterial cell wall biosynthesis.
|
| |
Nat Struct Biol,
2,
644-653.
|
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|
PDB code:
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|
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V.E.Shevchik,
I.Bortoli-German,
J.Robert-Baudouy,
S.Robinet,
F.Barras,
and
G.Condemine
(1995).
Differential effect of dsbA and dsbC mutations on extracellular enzyme secretion in Erwinia chrysanthemi.
|
| |
Mol Microbiol,
16,
745-753.
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F.Jurnak,
M.D.Yoder,
R.Pickersgill,
and
J.Jenkins
(1994).
Parallel beta-domains: a new fold in protein structures.
|
| |
Curr Opin Struct Biol,
4,
802-806.
|
|
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|
R.Pickersgill,
J.Jenkins,
G.Harris,
W.Nasser,
and
J.Robert-Baudouy
(1994).
The structure of Bacillus subtilis pectate lyase in complex with calcium.
|
| |
Nat Struct Biol,
1,
717-723.
|
|
|
PDB code:
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|
|
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C.Chothia,
and
A.G.Murzin
(1993).
New folds for all-beta proteins.
|
| |
Structure,
1,
217-222.
|
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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
