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protein metals links
Lyase PDB id
1bn8
Jmol
Contents
Protein chain
399 a.a. *
Metals
_CA
Waters ×209
* Residue conservation analysis
PDB id:
1bn8
Name: Lyase
Title: Bacillus subtilis pectate lyase
Structure: Protein (pectate lyase). Chain: a. Ec: 4.2.2.2
Source: Bacillus subtilis. Organism_taxid: 1423. Strain: s1103
Resolution:
1.80Å     R-factor:   0.179    
Authors: R.Pickersgill,G.Harris,J.Jenkins
Key ref: R.Pickersgill et al. (1994). The structure of Bacillus subtilis pectate lyase in complex with calcium. Nat Struct Biol, 1, 717-723. PubMed id: 7634076 DOI: 10.1038/nsb1094-717
Date:
31-Jul-98     Release date:   05-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P39116  (PLY_BACSU) -  Pectate lyase
Seq:
Struc: 		420 a.a.
399 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.

 

 
DOI no: 10.1038/nsb1094-717 Nat Struct Biol 1:717-723 (1994)
PubMed id: 7634076  
 
 
The structure of Bacillus subtilis pectate lyase in complex with calcium.
R.Pickersgill, J.Jenkins, G.Harris, W.Nasser, J.Robert-Baudouy.
 
  ABSTRACT  
 
We have solved the structure of the Bacillus subtilis pectate lyase (BsPel) in complex with calcium. The structure consists of a parallel beta-helix domain and a loop region. The alpha L-bounded beta-strand seen in BsPel is a new element of protein structure and its frequent occurrence suggests it is an important characteristic of the parallel beta-helix. A pronounced cleft is formed between the loops and the parallel beta-helix domain and we propose that this is the active site cleft. Calcium, essential for the activity of the enzyme, binds at the bottom of this cleft and an arginine residue close to the calcium, which is conserved across all pectin and pectate lyases, may be involved in catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20596756 S.Basu, A.Roy, A.Ghosh, A.Bera, D.Chattopadhyay, and K.Chakrabarti (2011).
Arg²³⁵ is an essential catalytic residue of Bacillus pumilus DKS1 pectate lyase to degum ramie fibre.
  Biodegradation, 22, 153-161.  
20543060 H.G.Ouattara, S.Reverchon, S.L.Niamke, and W.Nasser (2010).
Biochemical properties of pectate lyases produced by three different Bacillus strains isolated from fermenting cocoa beans and characterization of their cloned genes.
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18978091 N.Konno, K.Igarashi, N.Habu, M.Samejima, and A.Isogai (2009).
Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
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19916917 P.K.Yadav, V.K.Singh, S.Yadav, K.D.Yadav, and D.Yadav (2009).
In silico analysis of pectin lyase and pectinase sequences.
  Biochemistry (Mosc), 74, 1049-1055.  
19202269 W.Sukhumsiirchart, S.Kawanishi, W.Deesukon, K.Chansiri, H.Kawasaki, and T.Sakamoto (2009).
Purification, characterization, and overexpression of thermophilic pectate lyase of Bacillus sp. RN1 isolated from a Hot Spring in Thailand.
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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
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.
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PDB codes: 2v8i 2v8j 2v8k
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
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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.
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PDB code: 1pxz
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.
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15264254 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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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
14670977 J.Jenkins, V.E.Shevchik, N.Hugouvieux-Cotte-Pattat, and R.W.Pickersgill (2004).
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
  J Biol Chem, 279, 9139-9145.
PDB code: 1ru4
12540845 S.R.Herron, R.D.Scavetta, M.Garrett, M.Legner, and F.Jurnak (2003).
Characterization and implications of Ca2+ binding to pectate lyase C.
  J Biol Chem, 278, 12271-12277.
PDB codes: 1o88 1o8d 1o8e 1o8f 1o8g 1o8h 1o8i 1o8j 1o8k 1o8l 1o8m
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.  
12221284 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.
PDB codes: 1gxm 1gxn 1gxo
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.  
11544130 F.Micheli (2001).
Pectin methylesterases: cell wall enzymes with important roles in plant physiology.
  Trends Plant Sci, 6, 414-419.  
  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
11302165 M.Takao, T.Nakaniwa, K.Yoshikawa, T.Terashita, and T.Sakai (2001).
Molecular cloning, DNA sequence, and expression of the gene encoding for thermostable pectate lyase of thermophilic Bacillus sp. TS 47.
  Biosci Biotechnol Biochem, 65, 322-329.  
11157235 W.Hashimoto, H.Miki, N.Tsuchiya, H.Nankai, and K.Murata (2001).
Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1.
  Appl Environ Microbiol, 67, 713-720.  
11272816 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.
  Biosci Biotechnol Biochem, 65, 133-142.  
10923781 A.Ogawa, K.Sawada, K.Saito, Y.Hakamada, N.Sumitomo, Y.Hatada, T.Kobayashi, and S.Ito (2000).
A new high-alkaline and high-molecular-weight pectate lyase from a Bacillus isolate: enzymatic properties and cloning of the gene for the enzyme.
  Biosci Biotechnol Biochem, 64, 1133-1141.  
11123920 D.E.Kamen, Y.Griko, and R.W.Woody (2000).
The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
  Biochemistry, 39, 15932-15943.  
11112543 J.A.Benen, H.C.Kester, L.Parenicová, and J.Visser (2000).
Characterization of Aspergillus niger pectate lyase A.
  Biochemistry, 39, 15563-15569.  
11193403 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.
  Biosci Biotechnol Biochem, 64, 2360-2367.  
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.  
10759850 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.
  Eur J Biochem, 267, 2268-2275.  
  10368144 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.  
  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.  
10052123 T.Kobayashi, K.Koike, T.Yoshimatsu, N.Higaki, A.Suzumatsu, T.Ozawa, Y.Hatada, and S.Ito (1999).
Purification and properties of a low-molecular-weight, high-alkaline pectate lyase from an alkaliphilic strain of Bacillus.
  Biosci Biotechnol Biochem, 63, 65-72.  
10216231 T.Kobayashi, Y.Hatada, N.Higaki, D.D.Lusterio, T.Ozawa, K.Koike, S.Kawai, and S.Ito (1999).
Enzymatic properties and deduced amino acid sequence of a high-alkaline pectate lyase from an alkaliphilic Bacillus isolate.
  Biochim Biophys Acta, 1427, 145-154.  
10427684 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.
  Biosci Biotechnol Biochem, 63, 998.  
10521427 Y.van Santen, J.A.Benen, K.H.Schröter, K.H.Kalk, S.Armand, J.Visser, and B.W.Dijkstra (1999).
1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.
  J Biol Chem, 274, 30474-30480.
PDB code: 1czf
9680962 C.Domingo, K.Roberts, N.J.Stacey, I.Connerton, F.Ruíz-Teran, and M.C.McCann (1998).
A pectate lyase from Zinnia elegans is auxin inducible.
  Plant J, 13, 17-28.  
9733763 R.Pickersgill, D.Smith, K.Worboys, and J.Jenkins (1998).
Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
  J Biol Chem, 273, 24660-24664.
PDB code: 1bhe
9636063 S.Miller, B.Schuler, and R.Seckler (1998).
A reversibly unfolding fragment of P22 tailspike protein with native structure: the isolated beta-helix domain.
  Biochemistry, 37, 9160-9168.  
9204285 J.Heringa, and W.R.Taylor (1997).
Three-dimensional domain duplication, swapping and stealing.
  Curr Opin Struct Biol, 7, 416-421.  
  9195887 O.Mayans, M.Scott, I.Connerton, T.Gravesen, J.Benen, J.Visser, R.Pickersgill, and J.Jenkins (1997).
Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases.
  Structure, 5, 677-689.
PDB codes: 1idj 1idk
  9115442 T.N.Petersen, S.Kauppinen, and S.Larsen (1997).
The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.
  Structure, 5, 533-544.
PDB code: 1rmg
  8665839 C.Kisker, H.Schindelin, B.E.Alber, J.G.Ferry, and D.C.Rees (1996).
A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila.
  EMBO J, 15, 2323-2330.
PDB code: 1thj
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.  
7583641 B.Kobe, and J.Deisenhofer (1995).
Proteins with leucine-rich repeats.
  Curr Opin Struct Biol, 5, 409-416.  
7654407 I.W.Sutherland (1995).
Polysaccharide lyases.
  FEMS Microbiol Rev, 16, 323-347.  
8556430 P.W.Goodenough (1995).
A review of protein engineering for the food industry.
  Mol Biotechnol, 4, 151-166.  
  8575190 S.Ernst, R.Langer, C.L.Cooney, and R.Sasisekharan (1995).
Enzymatic degradation of glycosaminoglycans.
  Crit Rev Biochem Mol Biol, 30, 387-444.  
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.  
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.