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PDBsum entry 1pcl

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Lyase (acting on polysaccharides) PDB id
1pcl
Jmol
Contents
Protein chain
355 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1pcl
Name: Lyase (acting on polysaccharides)
Title: Unusual structural features in the parallel beta-helix in pectate lyases
Structure: Pectate lyase e. Chain: a. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Gene: ppel748 of pelc
Resolution:
2.20Å     R-factor:   0.206    
Authors: S.E.Lietzke,N.T.Keen,F.Jurnak
Key ref:
M.D.Yoder et al. (1993). Unusual structural features in the parallel beta-helix in pectate lyases. Structure, 1, 241-251. PubMed id: 8081738 DOI: 10.1016/0969-2126(93)90013-7
Date:
05-Nov-93     Release date:   14-Feb-95    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04960  (PLYE1_ERWCH) -  Pectate lyase E
Seq:
Struc:
385 a.a.
355 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.4.2.2.2  - Pectate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pectin and Pectate Lyases
      Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pectin catabolic process   1 term 
  Biochemical function     lyase activity     3 terms  

 

 
DOI no: 10.1016/0969-2126(93)90013-7 Structure 1:241-251 (1993)
PubMed id: 8081738  
 
 
Unusual structural features in the parallel beta-helix in pectate lyases.
M.D.Yoder, S.E.Lietzke, F.Jurnak.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.
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.
 
  The above figures are reprinted by permission from Cell Press: Structure (1993, 1, 241-251) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20553501 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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20664542 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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20549800 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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19193645 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.
  J Biol Chem, 284, 10100-10109.
PDB codes: 3eqn 3eqo
18430740 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.
  J Biol Chem, 283, 18260-18268.
PDB codes: 3b4n 3b8y 3b90
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
18462681 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.
  Structure, 16, 766-775.
PDB codes: 2vbe 2vbk 2vbm
18214954 Q.R.Fan, and W.A.Hendrickson (2008).
Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.
  Proteins, 72, 393-401.  
17947240 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.
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
17881361 D.W.Abbott, and A.B.Boraston (2007).
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.
  J Biol Chem, 282, 35328-35336.
PDB codes: 2v8i 2v8j 2v8k
17372357 T.J.Oldfield (2007).
CAALIGN: a program for pairwise and multiple protein-structure alignment.
  Acta Crystallogr D Biol Crystallogr, 63, 514-525.  
16547930 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.
  Proteins, 63, 976-985.  
17023423 M.Margittai, and R.Langen (2006).
Side chain-dependent stacking modulates tau filament structure.
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16531237 P.Iengar, N.V.Joshi, and P.Balaram (2006).
Conformational and sequence signatures in beta helix proteins.
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16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
15539389 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.
  J Biol Chem, 280, 3740-3746.
PDB code: 1pxz
16060675 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.
  Biochemistry, 44, 10669-10680.  
15968068 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.
  J Bacteriol, 187, 4573-4583.  
15155751 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.
  J Biol Chem, 279, 32882-32896.
PDB codes: 1ofl 1ofm
15159558 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.
  Acta Crystallogr D Biol Crystallogr, 60, 999.
PDB code: 1r76
12424253 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.
  J Biol Chem, 278, 1542-1548.  
12962629 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.
  Structure, 11, 1111-1121.
PDB codes: 1ogm 1ogo
12777771 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.  
12832805 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.
  Acta Crystallogr D Biol Crystallogr, 59, 1339-1342.
PDB codes: 1ooc 1pe9
12475987 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.
PDB codes: 1j0m 1j0n
12015881 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.  
12037303 L.M.Thomas, C.N.Doan, R.L.Oliver, and M.D.Yoder (2002).
Structure of pectate lyase A: comparison to other isoforms.
  Acta Crystallogr D Biol Crystallogr, 58, 1008-1015.
PDB codes: 1jrg 1jta
11914504 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.  
11504559 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.  
  11493601 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.
  J Biol Chem, 276, 40202-40209.
PDB code: 1h80
11717490 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
  Acta Crystallogr D Biol Crystallogr, 57, 1786-1792.
PDB code: 1ee6
11752429 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.  
11222281 S.P.Graether, and Z.Jia (2001).
Modeling Pseudomonas syringae ice-nucleation protein as a beta-helical protein.
  Biophys J, 80, 1169-1173.  
10899428 L.C.Serpell (2000).
Alzheimer's amyloid fibrils: structure and assembly.
  Biochim Biophys Acta, 1502, 16-30.  
10818352 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2000).
Crystallization and preliminary X-ray analysis of high-alkaline pectate lyase.
  Acta Crystallogr D Biol Crystallogr, 56, 749-750.
PDB code: 1ee6
10922032 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.
  Proc Natl Acad Sci U S A, 97, 8762-8769.  
11018131 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.
  Annu Rev Microbiol, 54, 289-340.  
10428949 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.
  EMBO J, 18, 4096-4107.
PDB codes: 1fwy 1fxj
  10198006 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.
  J Bacteriol, 181, 2440-2447.  
10089492 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.
  Acta Crystallogr D Biol Crystallogr, 54, 1155-1167.  
  9537364 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.  
9826605 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.  
9241431 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.  
  8975898 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.  
  9098045 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.  
  9393696 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.  
8946845 B.Kobe (1996).
Leucines on a roll.
  Nat Struct Biol, 3, 977-980.  
8805583 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.  
8900122 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.  
8621711 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.  
7583641 B.Kobe, and J.Deisenhofer (1995).
Proteins with leucine-rich repeats.
  Curr Opin Struct Biol, 5, 409-416.  
8577252 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.  
  8575190 S.Ernst, R.Langer, C.L.Cooney, and R.Sasisekharan (1995).
Enzymatic degradation of glycosaminoglycans.
  Crit Rev Biochem Mol Biol, 30, 387-444.  
7552726 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.
PDB code: 1mbr
7476168 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.  
7712282 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.  
7634076 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: 1bn8
8081735 C.Chothia, and A.G.Murzin (1993).
New folds for all-beta proteins.
  Structure, 1, 217-222.  
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.