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PDBsum entry 1epo
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Hydrolase/hydrolase inhibitor PDB id
1epo

 

 

 

 

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Contents
Protein chain
330 a.a. *
Ligands
2Z3
Waters ×306
* Residue conservation analysis
PDB id:
1epo
Name: Hydrolase/hydrolase inhibitor
Title: Endothia aspartic proteinase (endothiapepsin) complexed with cp-81,282 (mor phe nle chf nme)
Structure: Endothiapepsin. Chain: e. Engineered: yes
Source: Cryphonectria parasitica. Chestnut blight fungus. Organism_taxid: 5116
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.180    
Authors: B.Veerapandian,J.B.Cooper,T.L.Blundell
Key ref:
B.Veerapandian et al. (1992). Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases. Protein Sci, 1, 322-328. PubMed id: 1304340 DOI: 10.1002/pro.5560010303
Date:
27-Jul-94     Release date:   20-Dec-94    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11838  (CARP_CRYPA) -  Endothiapepsin from Cryphonectria parasitica
Seq:
Struc: 		419 a.a.
330 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.23.22  - endothiapepsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity similar to that of pepsin A, preferring hydrophobic residues at P1 and P1', but does not cleave 14-Ala-|-Leu-15 in the B chain of insulin or Z-Glu-Tyr. Clots milk.

 

 
DOI no: 10.1002/pro.5560010303 Protein Sci 1:322-328 (1992)
PubMed id: 1304340  
 
 
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.
B.Veerapandian, J.B.Cooper, A.Sali, T.L.Blundell, R.L.Rosati, B.W.Dominy, D.B.Damon, D.J.Hoover.
 
  ABSTRACT  
 
We report the X-ray analysis at 2.0 A resolution for crystals of the aspartic proteinase endothiapepsin (EC 3.4.23.6) complexed with a potent difluorostatone-containing tripeptide renin inhibitor (CP-81,282). The scissile bond surrogate, an electrophilic ketone, is hydrated in the complex. The pro-(R) (statine-like) hydroxyl of the tetrahedral carbonyl hydrate is hydrogen-bonded to both active-site aspartates 32 and 215 in the position occupied by a water in the native enzyme. The second hydroxyl oxygen of the hydrate is hydrogen-bonded only to the outer oxygen of Asp 32. These experimental data provide a basis for a model of the tetrahedral intermediate in aspartic proteinase-mediated cleavage of the amide bond. This indicates a mechanism in which Asp 32 is the proton donor and Asp 215 carboxylate polarizes a bound water for nucleophilic attack. The mechanism involves a carboxylate (Asp 32) that is stabilized by extensive hydrogen bonding, rather than an oxyanion derivative of the peptide as in serine proteinase catalysis.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Thestereochemistryandinteractionsofthetetrahedralhydratewiththeenzyme.Interatomicdistancesaretakenfrom therefinedStructure, hasanestimatedcoordinateerrorof 0.2 A. Theinputfor aGaussian 88 calculationwascreated from heX-raypositionsforthecarboxygroupsofAsp 2 and 215, and, from thestatineresidue,thetwohydroxyloxygens, thetwofluorines,andthetwocarbonstheyareattachedto.Hydrogenatomswerethenaddedusingstandardbondlengthsand anglestoformtwopossiblecomplexes(theoneshown,andanalternativearrangement in whichAsp 2 is protonatedandAp 215 charged). 		Figure 4.
Fig. 4. proposed mechanism for proteolytic cleavage of the amide bond by an aspartic proteinase.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1992, 1, 322-328) copyright 1992.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19763297 C.Fäh, L.A.Hardegger, L.Baitsch, W.B.Schweizer, S.Meyer, D.Bur, and F.Diederich (2009).
New organofluorine building blocks: inhibition of the malarial aspartic proteases plasmepsin II and IV by alicyclic alpha,alpha-difluoroketone hydrates.
  Org Biomol Chem, 7, 3947-3957.  
  18296260 A.Minarowska, M.Gacko, A.Karwowska, and Ć..Minarowski (2008).
Human cathepsin D.
  Folia Histochem Cytobiol, 46, 23-38.  
18675276 A.S.Nascimento, S.Krauchenco, A.M.Golubev, A.Gustchina, A.Wlodawer, and I.Polikarpov (2008).
Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A.
  J Mol Biol, 382, 763-778.
PDB codes: 3c9x 3c9y 3emy
18479128 L.Coates, H.F.Tuan, S.Tomanicek, A.Kovalevsky, M.Mustyakimov, P.Erskine, and J.Cooper (2008).
The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction.
  J Am Chem Soc, 130, 7235-7237.
PDB codes: 2jji 2jjj 2vs2
  18084100 H.F.Tuan, P.Erskine, P.Langan, J.Cooper, and L.Coates (2007).
Preliminary neutron and ultrahigh-resolution X-ray diffraction studies of the aspartic proteinase endothiapepsin cocrystallized with a gem-diol inhibitor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1080-1083.  
16632493 K.Stierand, P.C.Maass, and M.Rarey (2006).
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams.
  Bioinformatics, 22, 1710-1716.  
16673078 L.Coates, P.T.Erskine, S.Mall, R.Gill, S.P.Wood, D.A.Myles, and J.B.Cooper (2006).
X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases.
  Eur Biophys J, 35, 559-566.  
19079786 N.Yu, S.A.Hayik, B.Wang, N.Liao, C.H.Reynolds, and K.M.Merz (2006).
Assigning the protonation states of the key aspartates in beta-Secretase using QM/MM X-ray structure refinement.
  J Chem Theory Comput, 2, 1057-1069.  
15633197 A.Onoda, H.Yamamoto, Y.Yamada, K.Lee, S.Adachi, T.A.Okamura, K.Yoshizawa-Kumagaye, K.Nakajima, T.Kawakami, S.Aimoto, and N.Ueyama (2005).
Switching of turn conformation in an aspartate anion peptide fragment by NH . . . O- hydrogen bonds.
  Biopolymers, 80, 233-248.  
12876323 P.T.Erskine, L.Coates, S.Mall, R.S.Gill, S.P.Wood, D.A.Myles, and J.B.Cooper (2003).
Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides.
  Protein Sci, 12, 1741-1749.
PDB codes: 1oew 1oex
11714911 N.S.Andreeva, and L.D.Rumsh (2001).
Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes.
  Protein Sci, 10, 2439-2450.  
10842341 C.M.Stultz, and M.Karplus (2000).
Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin.
  Proteins, 40, 258-289.  
10666618 J.B.Cooper, and D.A.Myles (2000).
A preliminary neutron Laue diffraction study of the aspartic proteinase endothiapepsin.
  Acta Crystallogr D Biol Crystallogr, 56, 246-248.  
10089458 J.Yang, and J.W.Quail (1999).
Structure of the Rhizomucor miehei aspartic proteinase complexed with the inhibitor pepstatin A at 2.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 625-630.
PDB code: 2rmp
10200159 M.S.Wolfe, W.Xia, C.L.Moore, D.D.Leatherwood, B.Ostaszewski, T.Rahmati, I.O.Donkor, and D.J.Selkoe (1999).
Peptidomimetic probes and molecular modeling suggest that Alzheimer's gamma-secretase is an intramembrane-cleaving aspartyl protease.
  Biochemistry, 38, 4720-4727.  
10427707 U.M.Nasir, F.Suzuki, T.Nagai, T.Nakagawa, and Y.Nakamura (1999).
Tyrosine-83 of human renin contributes to biphasic pH dependence of the renin-angiotensinogen reaction.
  Biosci Biotechnol Biochem, 63, 1143-1145.  
9532792 U.M.Nasir, K.Takahashi, T.Nagai, T.Nakagawa, F.Suzuki, and Y.Nakamura (1998).
Two peaks in pH dependence of renin-angiotensinogen reaction.
  Biosci Biotechnol Biochem, 62, 338-340.  
9271500 G.S.Laco, C.Schalk-Hihi, J.Lubkowski, G.Morris, A.Zdanov, A.Olson, J.H.Elder, A.Wlodawer, and A.Gustchina (1997).
Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor.
  Biochemistry, 36, 10696-10708.
PDB codes: 2fiv 3fiv
9342349 M.Kobayashi, Y.Fujiwara, M.Goda, H.Komeda, and S.Shimizu (1997).
Identification of active sites in amidase: evolutionary relationship between amide bond- and peptide bond-cleaving enzymes.
  Proc Natl Acad Sci U S A, 94, 11986-11991.  
8778779 A.Beveridge (1996).
A theoretical study of torsional flexibility in the active site of aspartic proteinases: implications for catalysis.
  Proteins, 24, 322-334.  
8913621 G.Iliadis, B.Brzezinski, and G.Zundel (1996).
Aspartic proteinases: Fourier transform infrared spectroscopic studies of a model of the active side.
  Biophys J, 71, 2840-2847.  
8841139 R.B.Rose, C.S.Craik, N.L.Douglas, and R.M.Stroud (1996).
Three-dimensional structures of HIV-1 and SIV protease product complexes.
  Biochemistry, 35, 12933-12944.
PDB codes: 1ytg 1yth 1yti 1ytj
9007691 S.OƂdziej, and J.Ciarkowski (1996).
Mechanism of action of aspartic proteinases: application of transition-state analogue theory.
  J Comput Aided Mol Des, 10, 583-588.  
  7703859 D.Bailey, and J.B.Cooper (1994).
A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica.
  Protein Sci, 3, 2129-2143.
PDB codes: 1epl 1epm 1epn 1epr 1eqs
8259000 S.S.Abdel-Meguid (1993).
Inhibitors of aspartyl proteinases.
  Med Res Rev, 13, 731-778.  
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.

 

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