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Glycosidase PDB id
1bhe
Jmol
Contents
Protein chain
376 a.a. *
Waters ×295
* Residue conservation analysis
PDB id:
1bhe
Name: Glycosidase
Title: Polygalacturonase from erwinia carotovora ssp. Carotovora
Structure: Polygalacturonase. Chain: a. Synonym: peha. Engineered: yes
Source: Pectobacterium carotovorum subsp. Carotovorum. Organism_taxid: 555. Strain: subsp. Carotovorum. Expressed in: bacillus subtilis. Expression_system_taxid: 1423. Other_details: see h. Hemila, r. Pakkanen, r. Heikinheimo, e. Tapio palva & i. Palva (1992) gene 116, 27-33
Resolution:
1.90Å     R-factor:   0.198     R-free:   0.239
Authors: R.Pickersgill,D.Smith,K.Worboys,J.Jenkins
Key ref:
R.Pickersgill et al. (1998). Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. J Biol Chem, 273, 24660-24664. PubMed id: 9733763 DOI: 10.1074/jbc.273.38.24660
Date:
05-Jun-98     Release date:   11-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26509  (PGLR2_PECCC) -  Endo-polygalacturonase
Seq:
Struc: 		402 a.a.
376 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.15  - Polygalacturonase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1074/jbc.273.38.24660 J Biol Chem 273:24660-24664 (1998)
PubMed id: 9733763  
 
 
Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
R.Pickersgill, D.Smith, K.Worboys, J.Jenkins.
 
  ABSTRACT  
 
The crystal structure of the 40-kDa endo-polygalacturonase from Erwinia carotovora ssp. carotovora was solved by multiple isomorphous replacement and refined at 1.9 A to a conventional crystallographic R-factor of 0.198 and Rfree of 0.239. This is the first structure of a polygalacturonase and comprises a 10 turn right-handed parallel beta-helix domain with two loop regions forming a "tunnel like" substrate-binding cleft. Sequence conservation indicates that the active site of polygalacturonase is between these two loop regions, and comparison of the structure of polygalacturonase with that of rhamnogalacturonase A from Aspergillus aculeatus enables two conserved aspartates, presumed to be catalytic residues, to be identified. An adjacent histidine, in accord with biochemical results, is also seen. A similarity in overall electrostatic properties of the substrate-binding clefts of polygalacturonase and pectate lyase, which bind and cleave the same substrate, polygalacturonic acid, is also revealed.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Schematic representation of the structures of E. carotovora ssp. carotovora polygalacturonase (PehA) (A), A. aculeatus rhamnogalacturonase A (RGase A) (B), and B. subtilis pectate lyase (BsPel) (C). The parallel -sheets PB1, PB1a, PB2, and PB3 are yellow, blue, green, and red, respectively. PehA and RGase A have 10 complete turns of right-handed parallel -helix architecture, BsPel has seven turns and lacks PB1a. D, the active site of PehA is on the surface of parallel -sheet one, on -strands four, five, six, seven, and eight, and on the loops that precede these -strands. Aspartates 202 and 223 are conserved in all polygalacturonases and in RGase A (see also Fig. 4). This figure was prepared using MOLSCRIPT (41). 		Figure 3.
Fig. 3. Electrostatic potential of PehA calculated using GRASP (42) and contoured at +12.5 (blue) and 12.5 (red) mV. This view is looking down, between the long loop regions, onto the substrate-binding cleft, which runs from left to right. The substrate-binding cleft is predominantly positive (blue) apart from the active site comprising several aspartates (red, in center of this picture; see also Fig. 4A). The active site is between two lysine-rich loop regions. The positive potential is similar to that seen in BsPel with calcium bound (22) and dissimilar from that of pectin lyase (22) or RGase A (6).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 24660-24664) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19653129 S.Aminzadeh, H.Naderi-Manesh, K.Khajeh, B.Ranjbar, and N.Farrokhi (2010).
Characterization of acid-induced partially folded conformation resembling a molten globule state of polygalacturonase from a filamentous fungus Tetracoccosporium sp.
  Appl Biochem Biotechnol, 160, 1921-1932.  
17876815 D.Bonivento, D.Pontiggia, A.D.Matteo, J.Fernandez-Recio, G.Salvi, D.Tsernoglou, F.Cervone, G.D.Lorenzo, and L.Federici (2008).
Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.
  Proteins, 70, 294-299.
PDB code: 2iq7
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
  18607098 P.B.Vordtriede, and M.D.Yoder (2008).
Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 645-647.  
18704748 Z.Xiao, S.Wang, H.Bergeron, J.Zhang, and P.C.Lau (2008).
A flax-retting endopolygalacturonase-encoding gene from Rhizopus oryzae.
  Antonie Van Leeuwenhoek, 94, 563-571.  
16452425 A.Wietzorrek, H.Schwarz, C.Herrmann, and V.Braun (2006).
The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1.
  J Bacteriol, 188, 1419-1436.  
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
16262687 L.D.Kluskens, G.J.van Alebeek, J.Walther, A.G.Voragen, W.M.de Vos, and J.van der Oost (2005).
Characterization and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritima.
  FEBS J, 272, 5464-5473.  
16259040 M.Xie, G.H.Krooshof, J.A.Benen, J.A.Atwood, D.King, C.Bergmann, and R.Orlando (2005).
Post-translational modifications of recombinant B. cinerea EPG 6.
  Rapid Commun Mass Spectrom, 19, 3389-3397.  
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.  
14997537 J.K.Choi, B.H.Lee, C.H.Chae, and W.Shin (2004).
Computer modeling of the rhamnogalacturonase-"hairy" pectin complex.
  Proteins, 55, 22-33.  
12904578 A.Di Matteo, L.Federici, B.Mattei, G.Salvi, K.A.Johnson, C.Savino, G.De Lorenzo, D.Tsernoglou, and F.Cervone (2003).
The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense.
  Proc Natl Acad Sci U S A, 100, 10124-10128.
PDB code: 1ogq
  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
14646066 S.Heffron, S.Watkins, R.Moeller, A.H.Taban, R.Butowt, D.DellaPenna, and F.Jurnak (2003).
Resolving the space-group ambiguity of crystals of tomato fruit polygalacturonase.
  Acta Crystallogr D Biol Crystallogr, 59, 2088-2093.  
  15841240 Z.Shen, M.Denton, N.Mutti, K.Pappan, M.R.Kanost, J.C.Reese, and G.R.Reeck (2003).
Polygalacturonase from Sitophilus oryzae: possible horizontal transfer of a pectinase gene from fungi to weevils.
  J Insect Sci, 3, 24.  
12236597 A.Götesson, J.S.Marshall, D.A.Jones, and A.R.Hardham (2002).
Characterization and evolutionary analysis of a large polygalacturonase gene family in the oomycete plant pathogen Phytophthora cinnamomi.
  Mol Plant Microbe Interact, 15, 907-921.  
  12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
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.  
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.  
11929517 T.Palomäki, R.Pickersgill, R.Riekki, M.Romantschuk, and H.T.Saarilahti (2002).
A putative three-dimensional targeting motif of polygalacturonase (PehA), a protein secreted through the type II (GSP) pathway in Erwinia carotovora.
  Mol Microbiol, 43, 585-596.  
12022868 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2002).
Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
  Biochemistry, 41, 6651-6659.
PDB codes: 1k5c 1kcc 1kcd
11544130 F.Micheli (2001).
Pectin methylesterases: cell wall enzymes with important roles in plant physiology.
  Trends Plant Sci, 6, 414-419.  
11687632 L.Federici, C.Caprari, B.Mattei, C.Savino, A.Di Matteo, G.De Lorenzo, F.Cervone, and D.Tsernoglou (2001).
Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).
  Proc Natl Acad Sci U S A, 98, 13425-13430.
PDB code: 1hg8
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
11157954 M.Göttfert, S.Röthlisberger, C.Kündig, C.Beck, R.Marty, and H.Hennecke (2001).
Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome.
  J Bacteriol, 183, 1405-1412.  
11168425 S.K.Niture, A.Pant, and A.R.Kumar (2001).
Active site characterization of the single endo-polygalacturonase produced by Fusarium moniliforme NCIM 1276.
  Eur J Biochem, 268, 832-840.  
11468409 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2001).
Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum.
  Acta Crystallogr D Biol Crystallogr, 57, 1171-1173.  
11223531 T.Tada, C.T.Lu, Y.Nakamura, K.Wada, I.Miyahara, K.Hirotsu, Y.Katsuya, M.Sawada, M.Takao, T.Sakai, and K.Nishimura (2001).
Crystallization and preliminary X-ray analysis of a novel pectolytic enzyme, polymethoxygalacturonase SX1 from Trichosporon penicillatum.
  Acta Crystallogr D Biol Crystallogr, 57, 457-458.  
11092941 C.T.Lu, T.Tada, Y.Nakamura, K.Wada, K.Nishimura, Y.Katsuya, M.Sawada, M.Takao, and T.Sakai (2000).
Crystallization and preliminary X-ray analysis of endopolygalacturonase SE1 from Trichosporon penicillatum.
  Acta Crystallogr D Biol Crystallogr, 56, 1668-1669.  
11112543 J.A.Benen, H.C.Kester, L.Parenicová, and J.Visser (2000).
Characterization of Aspergillus niger pectate lyase A.
  Biochemistry, 39, 15563-15569.  
  11206055 J.F.Kreisberg, S.D.Betts, and J.King (2000).
Beta-helix core packing within the triple-stranded oligomerization domain of the P22 tailspike.
  Protein Sci, 9, 2338-2343.  
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.  
10759864 T.Shimizu, K.Miyairi, and T.Okuno (2000).
Determination of glycosylation sites, disulfide bridges, and the C-terminus of Stereum purpureum mature endopolygalacturonase I by electrospray ionization mass spectrometry.
  Eur J Biochem, 267, 2380-2389.  
10930840 W.Huang, A.Matte, S.Suzuki, N.Sugiura, H.Miyazono, and M.Cygler (2000).
Crystallization and preliminary X-ray analysis of chondroitin sulfate ABC lyases I and II from Proteus vulgaris.
  Acta Crystallogr D Biol Crystallogr, 56, 904-906.  
10393307 L.Federici, B.Mattei, C.Caprari, C.Savino, F.Cervone, and D.Tsernoglou (1999).
Crystallization and preliminary X-ray diffraction study of the endo-polygalacturonase from Fusarium moniliforme.
  Acta Crystallogr D Biol Crystallogr, 55, 1359-1361.  
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 code is shown on the right.