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PDBsum entry 2apr

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Hydrolase (aspartic proteinase) PDB id
2apr
Jmol
Contents
Protein chain
325 a.a. *
Metals
_CA
Waters ×373
* Residue conservation analysis
PDB id:
2apr
Name: Hydrolase (aspartic proteinase)
Title: Structure and refinement at 1.8 angstroms resolution of the aspartic proteinase from rhizopus chinensis
Structure: Rhizopuspepsin. Chain: a. Engineered: yes
Source: Rhizopus microsporus var. Chinensis. Organism_taxid: 4843. Strain: var. Chinensis
Resolution:
1.80Å     R-factor:   0.143    
Authors: K.Suguna,D.R.Davies
Key ref: K.Suguna et al. (1987). Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis. J Mol Biol, 196, 877-900. PubMed id: 3316666
Date:
19-Mar-87     Release date:   16-Jul-87    
Supersedes: 1apr
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06026  (CARP_RHICH) -  Rhizopuspepsin
Seq:
Struc:
393 a.a.
325 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.23.21  - Rhizopuspepsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity similar to that of pepsin A, preferring hydrophobic residues at P1 and P1'. Clots milk and activates trypsinogen. Does not cleave 4-Gln-|-His-5, but does cleave 10-His-|-Leu-11 and 12-Val-|-Glu-13 in B chain of insulin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     aspartic-type endopeptidase activity     1 term  

 

 
J Mol Biol 196:877-900 (1987)
PubMed id: 3316666  
 
 
Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
K.Suguna, R.R.Bott, E.A.Padlan, E.Subramanian, S.Sheriff, G.H.Cohen, D.R.Davies.
 
  ABSTRACT  
 
The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 A, and for angle distances it is 0.034 A. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile "flap", a beta-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20367613 A.M.Kargatov, and A.V.Efimov (2010).
A novel structural motif and structural trees for proteins containing it.
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19180449 K.S.Keating, S.C.Flores, M.B.Gerstein, and L.A.Kuhn (2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
  Protein Sci, 18, 359-371.  
18294125 A.V.Efimov (2008).
Structural trees for proteins containing phi-motifs.
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18698471 T.Matsuhira, K.Tsuchihashi, H.Yamamoto, T.A.Okamura, and N.Ueyama (2008).
Novel photosystem involving protonation and deprotonation processes modelled on a PYP photocycle.
  Org Biomol Chem, 6, 3118-3126.  
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.  
15869381 D.Davies, and D.Davies (2005).
A quiet life with proteins.
  Annu Rev Biophys Biomol Struct, 34, 1.  
14501114 B.V.Prasad, and K.Suguna (2003).
Effect of pH on the structure of rhizopuspepsin.
  Acta Crystallogr D Biol Crystallogr, 59, 1755-1761.
PDB codes: 1uh7 1uh8 1uh9
11807249 B.V.Prasad, and K.Suguna (2002).
Role of water molecules in the structure and function of aspartic proteinases.
  Acta Crystallogr D Biol Crystallogr, 58, 250-259.  
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.  
11418762 S.W.Cho, N.Kim, M.U.Choi, and W.Shin (2001).
Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases.
  Acta Crystallogr D Biol Crystallogr, 57, 948-956.
PDB code: 1ibq
10830477 E.Ichishima (2000).
Unique catalytic and molecular properties of hydrolases from Aspergillus used in Japanese bioindustries.
  Biosci Biotechnol Biochem, 64, 675-688.  
10089409 P.D.Adams, N.S.Pannu, R.J.Read, and A.T.Brunger (1999).
Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement.
  Acta Crystallogr D Biol Crystallogr, 55, 181-190.  
10368289 R.M.Castillo, K.Mizuguchi, V.Dhanaraj, A.Albert, T.L.Blundell, and A.G.Murzin (1999).
A six-stranded double-psi beta barrel is shared by several protein superfamilies.
  Structure, 7, 227-236.  
9818265 A.T.Brünger, P.D.Adams, and L.M.Rice (1998).
Recent developments for the efficient crystallographic refinement of macromolecular structures.
  Curr Opin Struct Biol, 8, 606-611.  
  9521105 L.Hong, J.A.Hartsuck, S.Foundling, J.Ermolieff, and J.Tang (1998).
Active-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant.
  Protein Sci, 7, 300-305.
PDB code: 1axa
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
9335526 J.Symersky, M.Monod, and S.I.Foundling (1997).
High-resolution structure of the extracellular aspartic proteinase from Candida tropicalis yeast.
  Biochemistry, 36, 12700-12710.
PDB code: 1j71
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.  
8756522 I.A.Vakser (1996).
Low-resolution docking: prediction of complexes for underdetermined structures.
  Biopolymers, 39, 455-464.  
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.  
  7756993 A.A.Adzhubei, and M.J.Sternberg (1994).
Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building.
  Protein Sci, 3, 2395-2410.  
7731951 I.A.Vakser, and C.Aflalo (1994).
Hydrophobic docking: a proposed enhancement to molecular recognition techniques.
  Proteins, 20, 320-329.  
8464727 S.L.Moodie, and J.M.Thornton (1993).
A study into the effects of protein binding on nucleotide conformation.
  Nucleic Acids Res, 21, 1369-1380.  
8259000 S.S.Abdel-Meguid (1993).
Inhibitors of aspartyl proteinases.
  Med Res Rev, 13, 731-778.  
1603805 A.Sali, B.Veerapandian, J.B.Cooper, D.S.Moss, T.Hofmann, and T.L.Blundell (1992).
Domain flexibility in aspartic proteinases.
  Proteins, 12, 158-170.  
  1304340 B.Veerapandian, J.B.Cooper, A.Sali, T.L.Blundell, R.L.Rosati, B.W.Dominy, D.B.Damon, and D.J.Hoover (1992).
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.
  Protein Sci, 1, 322-328.
PDB code: 1epo
1332025 D.H.Ohlendorf, S.I.Foundling, J.J.Wendoloski, J.Sedlacek, P.Strop, and F.R.Salemme (1992).
Structural studies of the retroviral proteinase from avian myeloblastosis associated virus.
  Proteins, 14, 382-391.
PDB codes: 1mvp 2mvp
1549581 E.Katchalski-Katzir, I.Shariv, M.Eisenstein, A.A.Friesem, C.Aflalo, and I.A.Vakser (1992).
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
  Proc Natl Acad Sci U S A, 89, 2195-2199.  
  1304887 E.Meyer (1992).
Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.
  Protein Sci, 1, 1543-1562.  
1594574 J.A.Hartsuck, G.Koelsch, and S.J.Remington (1992).
The high-resolution crystal structure of porcine pepsinogen.
  Proteins, 13, 1.
PDB code: 3psg
1603809 K.Suguna, E.A.Padlan, R.Bott, J.Boger, K.D.Parris, and D.R.Davies (1992).
Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
  Proteins, 13, 195-205.
PDB codes: 4apr 5apr 6apr
  1303752 M.E.Karpen, P.L.de Haseth, and K.E.Neet (1992).
Differences in the amino acid distributions of 3(10)-helices and alpha-helices.
  Protein Sci, 1, 1333-1342.  
2062837 A.R.Karlström, and R.L.Levine (1991).
Copper inhibits the protease from human immunodeficiency virus 1 by both cysteine-dependent and cysteine-independent mechanisms.
  Proc Natl Acad Sci U S A, 88, 5552-5556.  
  1710977 A.Volbeda, A.Lahm, F.Sakiyama, and D.Suck (1991).
Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
  EMBO J, 10, 1607-1618.  
  1874000 C.Hutchins, and J.Greer (1991).
Comparative modeling of proteins in the design of novel renin inhibitors.
  Crit Rev Biochem Mol Biol, 26, 77.  
2062827 R.K.Wierenga, M.E.Noble, J.P.Postma, H.Groendijk, K.H.Kalk, W.G.Hol, and F.R.Opperdoes (1991).
The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase.
  Proteins, 10, 33-49.
PDB codes: 2tim 3tim
2217165 C.Abad-Zapatero, T.J.Rydel, and J.Erickson (1990).
Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.
  Proteins, 8, 62-81.
PDB code: 3pep
2281084 E.G.Hutchinson, and J.M.Thornton (1990).
HERA--a program to draw schematic diagrams of protein secondary structures.
  Proteins, 8, 203-212.  
2217166 G.L.Gilliland, E.L.Winborne, J.Nachman, and A.Wlodawer (1990).
The three-dimensional structure of recombinant bovine chymosin at 2.3 A resolution.
  Proteins, 8, 82.
PDB code: 1cms
2153583 J.K.Rao, and A.Wlodawer (1990).
Is the pseudo-dyad in retroviral proteinase monomers structural or evolutionary?
  FEBS Lett, 260, 201-205.  
2182390 R.M.Berka, M.Ward, L.J.Wilson, K.J.Hayenga, K.H.Kodama, L.P.Carlomagno, and S.A.Thompson (1990).
Molecular cloning and deletion of the gene encoding aspergillopepsin A from Aspergillus awamori.
  Gene, 86, 153-162.  
1963762 T.Beppu (1990).
Modification of milk-clotting aspartic proteinases by recombinant DNA techniques.
  Ann N Y Acad Sci, 613, 14-25.  
2184298 W.J.Greenlee (1990).
Renin inhibitors.
  Med Res Rev, 10, 173-236.  
  2676515 A.Sali, B.Veerapandian, J.B.Cooper, S.I.Foundling, D.J.Hoover, and T.L.Blundell (1989).
High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.
  EMBO J, 8, 2179-2188.
PDB code: 5er2
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.