PDBsum entry 1ee6

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protein metals links
Lyase PDB id
Protein chain
197 a.a. *
Waters ×170
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of pectate lyase from bacillus sp. Strain
Structure: Pectate lyase. Chain: a. Ec:
Source: Bacillus sp.. Organism_taxid: 98226. Strain: ksm-p15
2.30Å     R-factor:   0.186     R-free:   0.234
Authors: M.Akita,A.Suzuki,T.Kobayashi,S.Ito,T.Yamane
Key ref:
M.Akita et al. (2001). The first structure of pectate lyase belonging to polysaccharide lyase family 3. Acta Crystallogr D Biol Crystallogr, 57, 1786-1792. PubMed id: 11717490 DOI: 10.1107/S0907444901014482
31-Jan-00     Release date:   31-Jan-01    
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Protein chain
Pfam   ArchSchema ?
Q9RHW0  (Q9RHW0_BACSP) -  Pectate lyase
224 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     pectate lyase activity     1 term  


DOI no: 10.1107/S0907444901014482 Acta Crystallogr D Biol Crystallogr 57:1786-1792 (2001)
PubMed id: 11717490  
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
M.Akita, A.Suzuki, T.Kobayashi, S.Ito, T.Yamane.
The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.
  Selected figure(s)  
Figure 3.
Figure 3 Stereoview of the Pel-15 unique calcium-binding site formed by Asp80, Val81, Lys103 and three water molecules. One calcium-bound water molecule is bound to the O atom of Gly34 on the first T3. The location of this region is shown in Fig. 1-.
Figure 5.
Figure 5 Stereoviews of the T3-PB1 groove regions of (a) Pel-15 and (b) Ech-PelC (PDB entry [202]1air ). The location of this region is shown in Fig. 1[203] [link]-[204][turqarr.gif] . Amino-acid side chains are represented by stick models. The calcium ion and amino-acid side chains in the pH 9.5 structure are represented by a yellow sphere and red sticks, respectively. The conformations of those amino-acid side chains are changed by attachment of the calcium ion.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1786-1792) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21376731 C.Haupt, M.Bereza, S.T.Kumar, B.Kieninger, I.Morgado, P.Hortschansky, G.Fritz, C.Röcken, U.Horn, and M.Fändrich (2011).
Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils.
  J Mol Biol, 408, 529-540.  
19477900 M.Fauvart, N.Verstraeten, B.Dombrecht, R.Venmans, S.Beullens, C.Heusdens, and J.Michiels (2009).
Rhizobium etli HrpW is a pectin-degrading enzyme and differs from phytopathogenic homologues in enzymically crucial tryptophan and glycine residues.
  Microbiology, 155, 3045-3054.  
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 beta-propeller.
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
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
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
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
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
15136569 M.Yamasaki, S.Moriwaki, O.Miyake, W.Hashimoto, K.Murata, and B.Mikami (2004).
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
  J Biol Chem, 279, 31863-31872.
PDB code: 1vav
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
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
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
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.