PDBsum entry 1ge7

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Hydrolase PDB id
Protein chains
167 a.a. *
MAN ×2
_ZN ×2
Waters ×297
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Zinc peptidase from grifola frondosa
Structure: Peptidyl-lys metalloendopeptidase. Chain: a, b. Ec:
Source: Grifola frondosa. Organism_taxid: 5627. Tissue: fruiting body
2.00Å     R-factor:   0.179     R-free:   0.218
Authors: T.Hori,T.Kumasaka,M.Yamamoto,T.Nonaka,N.Tanaka,Y.Hashimoto, T.Ueki,K.Takio
Key ref:
T.Hori et al. (2001). Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. Acta Crystallogr D Biol Crystallogr, 57, 361-368. PubMed id: 11223512 DOI: 10.1107/S0907444900019740
11-Oct-00     Release date:   14-Mar-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P81054  (PLMP_GRIFR) -  Peptidyl-Lys metalloendopeptidase
348 a.a.
167 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptidyl-Lys metalloendopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage in proteins: Xaa-|-Lys (in which Xaa may be Pro).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metallopeptidase activity     2 terms  


DOI no: 10.1107/S0907444900019740 Acta Crystallogr D Biol Crystallogr 57:361-368 (2001)
PubMed id: 11223512  
Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.
T.Hori, T.Kumasaka, M.Yamamoto, N.Nonaka, N.Tanaka, Y.Hashimoto, U.Ueki, K.Takio.
Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.
  Selected figure(s)  
Figure 3.
Figure 3 Representative structures of the respective MEP families. (a) GfMEP, (b) neutrophil collagenase (Bode et al., 1994[Bode, W., Reinemer, P., Huber, R., Kleine, T., Schnierer, S. & Tschesche, H. (1994). EMBO J. 13, 1263-1269.]; metzincin; PDB code [230]1jap ) and (c) thermolysin (Holden et al., 1987[231] [Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H. & Matthews, B. W. (1987). Biochemistry, 26, 8542-8553.]-[232][bluearr.gif] ; gluzincin; PDB code [233]4tmn ). The S1' pocket region is coloured in blue and the zinc-binding site in red. The [234][alpha] -helices and [235][beta] -strands which compose the common folding topology among the three families are coloured cyan and magenta, respectively. The catalytic zinc ion and its ligand residues are also presented. Atoms are coloured with carbon in green, oxygen in red, nitrogen in blue and zinc in orange. All molecules are aligned in the same orientation with regard to the two ligand His residues and the zinc ion.
Figure 5.
Figure 5 The molecular-surface representation of the cleft region in the hexagonal crystals coloured according to their electrostatic potential: red for the electrostatically negative region and blue for the positive region. The molecular orientation is the same as in Fig. 2-. The molecular surface and electrostatic potential were calculated with GRASP (Nicholls et al., 1991[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.]).
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 361-368) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936200 C.Nakajima, H.Kuyama, T.Nakazawa, O.Nishimura, and S.Tsunasawa (2011).
A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry.
  Analyst, 136, 113-119.  
18952802 H.Arnadottir, I.Hvanndal, V.Andresdottir, S.E.Burr, J.Frey, and B.K.Gudmundsdottir (2009).
The AsaP1 peptidase of Aeromonas salmonicida subsp. achromogenes is a highly conserved deuterolysin metalloprotease (family M35) and a major virulence factor.
  J Bacteriol, 191, 403-410.  
19195997 L.Hohmann, C.Sherwood, A.Eastham, A.Peterson, J.K.Eng, J.S.Eddes, D.Shteynberg, and D.B.Martin (2009).
Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.
  J Proteome Res, 8, 1415-1422.  
15451101 J.H.Joh, B.G.Kim, W.S.Kong, Y.B.Yoo, N.K.Kim, H.R.Park, B.G.Cho, and C.S.Lee (2004).
Cloning and developmental expression of a metzincin family metalloprotease cDNA from oyster mushroom Pleurotus ostreatus.
  FEMS Microbiol Lett, 239, 57-62.  
12501439 T.Saito, N.Dohmae, M.Tsujimoto, and K.Takio (2002).
PCR cloning and heterologous expression of cDNA encoding a peptidyl-Lys metalloendopeptidase precursor of Grifola frondosa.
  J Gen Appl Microbiol, 48, 287-292.  
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.