DB code: D00440

RLCP classification 1.13.200.966 : Hydrolysis
CATH domain 2.40.70.10 : Cathepsin D, subunit A; domain 1 Catalytic domain
2.40.70.10 : Cathepsin D, subunit A; domain 1 Catalytic domain
E.C. 3.4.23.21
CSA 2apr
M-CSA 2apr
MACiE

CATH domain Related DB codes (homologues)
2.40.70.10 : Cathepsin D, subunit A; domain 1 D00471 D00436 D00438 D00439 D00441 D00442 D00443 D00437 D00444 D00423 D00445 D00484 M00206 M00166 D00231 D00529

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
P06026 Rhizopuspepsin
EC 3.4.23.21
A01.012 (Aspartic)
PF00026 (Asp)
[Graphical View]

KEGG enzyme name
rhizopuspepsin
Rhizopus aspartic proteinase
neurase
Rhizopus acid protease
Rhizopus acid proteinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P06026 CARP_RHICH 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.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00012 C00017 C00001 C00012 C00017 I00136
E.C.
Compound Peptide Protein H2O Peptide Protein Amino-diol-tetrahedral intermediate
Type peptide/protein peptide/protein H2O peptide/protein peptide/protein
ChEBI 15377
PubChem 22247451
962
2aprA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PRO-PHE-HIS-PUK-VAL-TYR (chain I) Unbound Unbound Unbound Unbound
4aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Transition-state-analogue:PRO-PHE-HIS-STA-LEU (chain I)
5aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Transition-state-analogue:PRO-PHE-CYS-STA-LEU-PHE-DHL (chain I)
6aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Transition-state-analogue:IVA-VAL-VAL-STA-ALA-STA (chain I)
2aprA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
4aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
5aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
6aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P06026

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2aprA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 35
3aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 35
4aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 35
5aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 35
6aprE01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 35
2aprA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 218
3aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 218
4aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 218
5aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 218
6aprE02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 218

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.5, p.7010-7012
[15]
Fig.8, p.8139
[26]
Fig.2, p.96-98

References
[1]
Resource
Comments
Medline ID
PubMed ID 596305
Journal Adv Exp Med Biol
Year 1977
Volume 95
Pages 33-41
Authors Subramanian E, Liu M, Swan ID, Davies DR
Title The crystal structure of an acid protease from Rhizopus chinensis at 2.5 A resolution.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID 77148881
PubMed ID 322132
Journal Proc Natl Acad Sci U S A
Year 1977
Volume 74
Pages 556-9
Authors Subramanian E, Swan ID, Liu M, Davies DR, Jenkins JA, Tickle IJ, Blundell TL
Title Homology among acid proteases: comparison of crystal structures at 3A resolution of acid proteases from Rhizopus chinensis and Endothia parasitica.
Related PDB
Related UniProtKB P06026
[3]
Resource
Comments
Medline ID
PubMed ID 6309756
Journal J Biochem (Tokyo)
Year 1983
Volume 93
Pages 1297-304
Authors Nakayama S, Nagashima Y, Hoshino M, Moriyama A, Takahashi K, Watanabe T, Yoshida M
Title Structural study on the active site of porcine pepsin and Rhizopus chinensis acid protease. Spin labeling with diazoketone reagents.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 88062720
PubMed ID 3316666
Journal J Mol Biol
Year 1987
Volume 196
Pages 877-900
Authors Suguna K, Bott RR, Padlan EA, Subramanian E, Sheriff S, Cohen GH, Davies DR
Title Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
Related PDB 2apr
Related UniProtKB P06026
[5]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 3313384
Journal Proc Natl Acad Sci U S A
Year 1987
Volume 84
Pages 7009-13
Authors Suguna K, Padlan EA, Smith CW, Carlson WD, Davies DR
Title Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
Related PDB 3apr
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3284587
Journal Biochemistry
Year 1988
Volume 27
Pages 1653-8
Authors Goldblum A
Title Theoretical calculations on the acidity of the active site in aspartic proteinases.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2693742
Journal J Mol Biol
Year 1989
Volume 210
Pages 785-811
Authors Summers NL, Karplus M
Title Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 2537531
Journal Science
Year 1989
Volume 243
Pages 928-31
Authors Weber IT, Miller M, Jaskolski M, Leis J, Skalka AM, Wlodawer A
Title Molecular modeling of the HIV-1 protease and its substrate binding site.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 2201571
Journal FEBS Lett
Year 1990
Volume 269
Pages 269-72
Authors Gustchina A, Weber IT
Title Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 2115087
Journal J Mol Biol
Year 1990
Volume 214
Pages 143-70
Authors Sielecki AR, Fedorov AA, Boodhoo A, Andreeva NS, James MN
Title Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 2217165
Journal Proteins
Year 1990
Volume 8
Pages 62-81
Authors Abad-Zapatero C, Rydel TJ, Erickson J
Title Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 1742463
Journal Biophys J
Year 1991
Volume 60
Pages 966-73
Authors Mao B
Title Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 2050673
Journal J Biol Chem
Year 1991
Volume 266
Pages 11718-25
Authors Chen Z, Koelsch G, Han HP, Wang XJ, Lin XL, Hartsuck JA, Tang J
Title Recombinant rhizopuspepsinogen. Expression, purification, and activation properties of recombinant rhizopuspepsinogens.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 1445256
Journal Biochem J
Year 1992
Volume 288
Pages 109-16
Authors Mao B
Title Molecular-dynamics investigation of molecular flexibility in ligand binding.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 1525154
Journal Biochemistry
Year 1992
Volume 31
Pages 8125-41
Authors Parris KD, Hoover DJ, Damon DB, Davies DR
Title Synthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 1526982
Journal J Biol Chem
Year 1992
Volume 267
Pages 18413-8
Authors Lin Y, Fusek M, Lin X, Hartsuck JA, Kezdy FJ, Tang J
Title pH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 1603809
Journal Proteins
Year 1992
Volume 13
Pages 195-205
Authors Suguna K, Padlan EA, Bott R, Boger J, Parris KD, Davies DR
Title Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
Related PDB 4apr 5apr 6apr
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 1455175
Journal Scand J Clin Lab Invest Suppl
Year 1992
Volume 210
Pages 127-35
Authors Tang J, Lin Y, Co E, Hartsuck JA, Lin X
Title Understanding HIV protease: can it be translated into effective therapy against AIDS?
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 8215428
Journal Arch Biochem Biophys
Year 1993
Volume 306
Pages 297-303
Authors Balbaa M, Cunningham A, Hofmann T
Title Secondary substrate binding in aspartic proteinases: contributions of subsites S3 and S'2 to kcat.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 8196057
Journal J Mol Biol
Year 1994
Volume 239
Pages 249-75
Authors Koehl P, Delarue M
Title Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 7854179
Journal Methods Enzymol
Year 1994
Volume 241
Pages 195-224
Authors Lin XL, Lin YZ, Tang J
Title Relationships of human immunodeficiency virus protease with eukaryotic aspartic proteases.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 7766059
Journal Phytochemistry
Year 1995
Volume 38
Pages 27-30
Authors Ichishima E, Ojima M, Yamagata Y, Hanzawa S, Nakamura T
Title Molecular and enzymatic properties of an aspartic proteinase from Rhizopus hangchow.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 8931128
Journal Protein Eng
Year 1996
Volume 9
Pages 885-93
Authors Nugent PG, Albert A, Orprayoon P, Wilsher J, Pitts JE, Blundell TL, Dhanaraj V
Title Protein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop from rhizopuspepsin.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 9561208
Journal Adv Exp Med Biol
Year 1998
Volume 436
Pages 115-21
Authors Kashparov IV, Popov ME, Popov EM
Title Mechanism of action of aspartic proteases.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 10419816
Journal Protein Expr Purif
Year 1999
Volume 16
Pages 213-20
Authors Flentke GR, Glinski J, Satyshur K, Rich DH
Title Purification and crystallization of rhizopuspepsin: the use of nickel chelation chromatography to select for catalytically active species.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11783905
Journal Appl Biochem Biotechnol
Year 2001
Volume 96
Pages 93-108
Authors Kalra P, Das A, Jayaram B
Title Free-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 11463304
Journal Org Lett
Year 2001
Volume 3
Pages 2313-6
Authors Dales NA, Bohacek RS, Satyshur KA, Rich DH
Title Design and synthesis of unsymmetrical peptidyl urea inhibitors of aspartic peptidases.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 11463303
Journal Org Lett
Year 2001
Volume 3
Pages 2309-12
Authors Ripka AS, Satyshur KA, Bohacek RS, Rich DH
Title Aspartic protease inhibitors designed from computer-generated templates bind as predicted.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 14501114
Journal Acta Crystallogr D Biol Crystallogr
Year 2003
Volume 59
Pages 1755-61
Authors Prasad BV, Suguna K
Title Effect of pH on the structure of rhizopuspepsin.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the peptidase family-A1.
According to the literature [5], the catalytic reaction proceeds as follows:
(1) Asp218 acts as a general base, abstracting a proton from a water molecule, which is bound between Asp35 and Asp218.
(2) The activated water, or the nucleophilic hydroxide ion, makes an attack on the carbonyl carbon atom of the substrate peptide bond, leading to the formation of a tetrahedral transition state with a negatively charged oxyanion (or gem-diol).
(3) The protonated carboxyl sidechain of Asp35 stabilzes the negative charge of the transition state.
(4) Asp218 acts as a general acid, protonating to the leaving amine group. This step leads to the cleavage of the peptide bond.

Created Updated
2004-10-27 2012-06-28