PDBsum entry 1kcd

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Hydrolase PDB id
Protein chain
333 a.a. *
NAG ×2
Waters ×520
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Endopolygalacturonase i from stereum purpureum complexed wit galacturonate at 1.15 a resolution.
Structure: Endopolygalacturonase. Chain: a. Fragment: residues 1-335. Ec:
Source: Chondrostereum purpureum. Organism_taxid: 58369. Strain: asp-4b
1.15Å     R-factor:   0.135     R-free:   0.071
Authors: T.Shimizu,T.Nakatsu,K.Miyairi,T.Okuno,H.Kato
Key ref:
T.Shimizu et al. (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. PubMed id: 12022868 DOI: 10.1021/bi025541a
08-Nov-01     Release date:   05-Jun-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P79074  (P79074_9AGAR) -  Endopolygalacturonase
403 a.a.
333 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     polygalacturonase activity     1 term  


DOI no: 10.1021/bi025541a Biochemistry 41:6651-6659 (2002)
PubMed id: 12022868  
Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, H.Kato.
Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19819900 M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2010).
Structural explanation for the acquisition of glycosynthase activity.
  J Biochem, 147, 237-244.
PDB codes: 2dro 2drq 2drr 2drs 3a3v
20208362 S.Ogawa, T.Shimizu, T.Kimura, K.Utoh, T.Okuno, and K.Miyairi (2010).
The pro-form of Stereum purpureum endopolygalacturonase I is inactivated by a pro-sequence in the C-terminal region.
  Biosci Biotechnol Biochem, 74, 558-562.  
18704933 C.H.da Silveira, D.E.Pires, R.C.Minardi, C.Ribeiro, C.J.Veloso, J.C.Lopes, W.Meira, G.Neshich, C.H.Ramos, R.Habesch, and M.M.Santoro (2009).
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins.
  Proteins, 74, 727-743.  
19490118 S.T.Philominathan, O.Matsushita, R.Gensure, and J.Sakon (2009).
Ca2+-induced linker transformation leads to a compact and rigid collagen-binding domain of Clostridium histolyticum collagenase.
  FEBS J, 276, 3589-3601.  
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.  
17372351 K.Fukuyama, and T.Okada (2007).
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron.
  Acta Crystallogr D Biol Crystallogr, 63, 472-477.
PDB codes: 2e39 2e3a 2e3b
16262687 L.D.Kluskens, G.J.van Alebeek, J.Walther, A.G.Voragen, 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.  
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.  
14573597 G.Golan, D.Shallom, A.Teplitsky, G.Zaide, S.Shulami, T.Baasov, V.Stojanoff, A.Thompson, Y.Shoham, and G.Shoham (2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
  J Biol Chem, 279, 3014-3024.
PDB codes: 1k9d 1k9e 1k9f 1l8n 1mqp 1mqq 1mqr
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
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.  
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
12876347 K.Takeda, H.Miyatake, N.Yokota, S.Matsuyama, H.Tokuda, and K.Miki (2003).
A practical phasing procedure using the MAD method without the aid of XAFS measurements: successful solution in the structure determination of the outer-membrane lipoprotein carrier LolA.
  Acta Crystallogr D Biol Crystallogr, 59, 1440-1446.  
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.