D00440
type: Enzyme
rlcp: p966
cath: Cathepsin D, subunit A; domain 1
ec: https://purl.uniprot.org/enzyme/3.4.23.21
csa: 2apr
uniprot: P06026
kegg enzyme: rhizopuspepsin
kegg enzyme: Rhizopus aspartic proteinase
kegg enzyme: neurase
kegg enzyme: Rhizopus acid protease
kegg enzyme: Rhizopus acid proteinase
kegg substrate: Peptide
kegg substrate: Protein
kegg substrate: H2O
kegg product: Peptide
kegg product: Protein
kegg intermediate: Amino-diol-tetrahedral intermediate
pdb: 2aprA01
pdb: 3aprE01
pdb: 4aprE01
pdb: 5aprE01
pdb: 6aprE01
pdb: 2aprA02
pdb: 3aprE02
pdb: 4aprE02
pdb: 5aprE02
pdb: 6aprE02
pdb bound state: Unbound
  compound: Peptide
  pdb: 2aprA01
pdb bound state: Analogue
  compound: Peptide
  pdb: 3aprE01
  ligand het code: PRO-PHE-HIS-PUK-VAL-TYR (chain I)
pdb bound state: Unbound
  compound: Peptide
  pdb: 4aprE01
pdb bound state: Unbound
  compound: Peptide
  pdb: 5aprE01
pdb bound state: Unbound
  compound: Peptide
  pdb: 6aprE01
pdb bound state: Unbound
  compound: Peptide
  pdb: 2aprA02
pdb bound state: Unbound
  compound: Peptide
  pdb: 3aprE02
pdb bound state: Unbound
  compound: Peptide
  pdb: 4aprE02
pdb bound state: Unbound
  compound: Peptide
  pdb: 5aprE02
pdb bound state: Unbound
  compound: Peptide
  pdb: 6aprE02
pdb bound state: Unbound
  compound: Protein
  pdb: 2aprA01
pdb bound state: Unbound
  compound: Protein
  pdb: 3aprE01
pdb bound state: Unbound
  compound: Protein
  pdb: 4aprE01
pdb bound state: Unbound
  compound: Protein
  pdb: 5aprE01
pdb bound state: Unbound
  compound: Protein
  pdb: 6aprE01
pdb bound state: Unbound
  compound: Protein
  pdb: 2aprA02
pdb bound state: Unbound
  compound: Protein
  pdb: 3aprE02
pdb bound state: Unbound
  compound: Protein
  pdb: 4aprE02
pdb bound state: Unbound
  compound: Protein
  pdb: 5aprE02
pdb bound state: Unbound
  compound: Protein
  pdb: 6aprE02
pdb bound state: Unbound
  compound: Peptide
  pdb: 2aprA01
pdb bound state: Unbound
  compound: Peptide
  pdb: 3aprE01
active site residues resources: P06026
references: Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.
references: Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor.
references: Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
references: Recombinant rhizopuspepsinogen. Expression, purification, and activation properties of recombinant rhizopuspepsinogens.
references: Molecular-dynamics investigation of molecular flexibility in ligand binding.
references: The crystal structure of an acid protease from Rhizopus chinensis at 2.5 A resolution.
references: Homology among acid proteases: comparison of crystal structures at 3A resolution of acid proteases from Rhizopus chinensis and Endothia parasitica.
references: Structural study on the active site of porcine pepsin and Rhizopus chinensis acid protease. Spin labeling with diazoketone reagents.
references: Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
references: Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
references: Theoretical calculations on the acidity of the active site in aspartic proteinases.
references: Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.
references: Molecular modeling of the HIV-1 protease and its substrate binding site.
references: Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap.
references: Synthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.
references: pH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants.
references: Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
references: Understanding HIV protease: can it be translated into effective therapy against AIDS?
references: Secondary substrate binding in aspartic proteinases: contributions of subsites S3 and S'2 to kcat.
references: Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.
references: Relationships of human immunodeficiency virus protease with eukaryotic aspartic proteases.
references: Molecular and enzymatic properties of an aspartic proteinase from Rhizopus hangchow.
references: Protein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop from rhizopuspepsin.
references: Mechanism of action of aspartic proteases.
references: Purification and crystallization of rhizopuspepsin: the use of nickel chelation chromatography to select for catalytically active species.
references: Free-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.
references: Design and synthesis of unsymmetrical peptidyl urea inhibitors of aspartic peptidases.
references: Aspartic protease inhibitors designed from computer-generated templates bind as predicted.
references: Effect of pH on the structure of rhizopuspepsin.
comment: 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.

Cathepsin D, subunit A; domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.40.70.10
catalytic domain: index.html

Peptide
type: KeggSubstrate
references: KEGG:C00012
compound type: peptide/protein
type: KeggProduct

Protein
type: KeggSubstrate
references: KEGG:C00017
compound type: peptide/protein
type: KeggProduct

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Amino-diol-tetrahedral intermediate
type: KeggIntermediate
references: KEGG:I00136

2aprA01
type: Pdb
references: 2apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2apr
catalytic residue: ASP 35

3aprE01
type: Pdb
references: 3apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3apr
catalytic residue: ASP 35

4aprE01
type: Pdb
references: 4apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:4apr
catalytic residue: ASP 35

5aprE01
type: Pdb
references: 5apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:5apr
catalytic residue: ASP 35

6aprE01
type: Pdb
references: 6apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:6apr
catalytic residue: ASP 35

2aprA02
type: Pdb
references: 2apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2apr
catalytic residue: ASP 218

3aprE02
type: Pdb
references: 3apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3apr
catalytic residue: ASP 218

4aprE02
type: Pdb
references: 4apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:4apr
catalytic residue: ASP 218

5aprE02
type: Pdb
references: 5apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:5apr
catalytic residue: ASP 218

6aprE02
type: Pdb
references: 6apr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:6apr
catalytic residue: ASP 218

Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2217165
journal: Proteins
volume: 8
pages: 62-81
published year: 1990
authors:
  item: Abad-Zapatero C
  item: Rydel TJ
  item: Erickson J

Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1742463
journal: Biophys J
volume: 60
pages: 966-73
published year: 1991
authors:
  item: Mao B

Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2115087
journal: J Mol Biol
volume: 214
pages: 143-70
published year: 1990
authors:
  item: Sielecki AR
  item: Fedorov AA
  item: Boodhoo A
  item: Andreeva NS
  item: James MN

Recombinant rhizopuspepsinogen. Expression, purification, and activation properties of recombinant rhizopuspepsinogens.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2050673
journal: J Biol Chem
volume: 266
pages: 11718-25
published year: 1991
authors:
  item: Chen Z
  item: Koelsch G
  item: Han HP
  item: Wang XJ
  item: Lin XL
  item: Hartsuck JA
  item: Tang J

Molecular-dynamics investigation of molecular flexibility in ligand binding.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1445256
journal: Biochem J
volume: 288
pages: 109-16
published year: 1992
authors:
  item: Mao B

The crystal structure of an acid protease from Rhizopus chinensis at 2.5 A resolution.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/596305
journal: Adv Exp Med Biol
volume: 95
pages: 33-41
published year: 1977
authors:
  item: Subramanian E
  item: Liu M
  item: Swan ID
  item: Davies DR

Homology among acid proteases: comparison of crystal structures at 3A resolution of acid proteases from Rhizopus chinensis and Endothia parasitica.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
medline id: 77148881
references: http://www.ncbi.nlm.nih.gov/pubmed/322132
journal: Proc Natl Acad Sci U S A
volume: 74
pages: 556-9
published year: 1977
authors:
  item: Subramanian E
  item: Swan ID
  item: Liu M
  item: Davies DR
  item: Jenkins JA
  item: Tickle IJ
  item: Blundell TL
references: P06026

Structural study on the active site of porcine pepsin and Rhizopus chinensis acid protease. Spin labeling with diazoketone reagents.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/6309756
journal: J Biochem (Tokyo)
volume: 93
pages: 1297-304
published year: 1983
authors:
  item: Nakayama S
  item: Nagashima Y
  item: Hoshino M
  item: Moriyama A
  item: Takahashi K
  item: Watanabe T
  item: Yoshida M

Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
medline id: 88062720
references: http://www.ncbi.nlm.nih.gov/pubmed/3316666
journal: J Mol Biol
volume: 196
pages: 877-900
published year: 1987
authors:
  item: Suguna K
  item: Bott RR
  item: Padlan EA
  item: Subramanian E
  item: Sheriff S
  item: Cohen GH
  item: Davies DR
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P06026

Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/3313384
journal: Proc Natl Acad Sci U S A
volume: 84
pages: 7009-13
published year: 1987
authors:
  item: Suguna K
  item: Padlan EA
  item: Smith CW
  item: Carlson WD
  item: Davies DR
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Theoretical calculations on the acidity of the active site in aspartic proteinases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3284587
journal: Biochemistry
volume: 27
pages: 1653-8
published year: 1988
authors:
  item: Goldblum A

Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2693742
journal: J Mol Biol
volume: 210
pages: 785-811
published year: 1989
authors:
  item: Summers NL
  item: Karplus M

Molecular modeling of the HIV-1 protease and its substrate binding site.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2537531
journal: Science
volume: 243
pages: 928-31
published year: 1989
authors:
  item: Weber IT
  item: Miller M
  item: Jaskolski M
  item: Leis J
  item: Skalka AM
  item: Wlodawer A

Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2201571
journal: FEBS Lett
volume: 269
pages: 269-72
published year: 1990
authors:
  item: Gustchina A
  item: Weber IT

Synthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1525154
journal: Biochemistry
volume: 31
pages: 8125-41
published year: 1992
authors:
  item: Parris KD
  item: Hoover DJ
  item: Damon DB
  item: Davies DR

pH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1526982
journal: J Biol Chem
volume: 267
pages: 18413-8
published year: 1992
authors:
  item: Lin Y
  item: Fusek M
  item: Lin X
  item: Hartsuck JA
  item: Kezdy FJ
  item: Tang J

Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/1603809
journal: Proteins
volume: 13
pages: 195-205
published year: 1992
authors:
  item: Suguna K
  item: Padlan EA
  item: Bott R
  item: Boger J
  item: Parris KD
  item: Davies DR
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Understanding HIV protease: can it be translated into effective therapy against AIDS?
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1455175
journal: Scand J Clin Lab Invest Suppl
volume: 210
pages: 127-35
published year: 1992
authors:
  item: Tang J
  item: Lin Y
  item: Co E
  item: Hartsuck JA
  item: Lin X

Secondary substrate binding in aspartic proteinases: contributions of subsites S3 and S'2 to kcat.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8215428
journal: Arch Biochem Biophys
volume: 306
pages: 297-303
published year: 1993
authors:
  item: Balbaa M
  item: Cunningham A
  item: Hofmann T

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8196057
journal: J Mol Biol
volume: 239
pages: 249-75
published year: 1994
authors:
  item: Koehl P
  item: Delarue M

Relationships of human immunodeficiency virus protease with eukaryotic aspartic proteases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7854179
journal: Methods Enzymol
volume: 241
pages: 195-224
published year: 1994
authors:
  item: Lin XL
  item: Lin YZ
  item: Tang J

Molecular and enzymatic properties of an aspartic proteinase from Rhizopus hangchow.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7766059
journal: Phytochemistry
volume: 38
pages: 27-30
published year: 1995
authors:
  item: Ichishima E
  item: Ojima M
  item: Yamagata Y
  item: Hanzawa S
  item: Nakamura T

Protein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop from rhizopuspepsin.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8931128
journal: Protein Eng
volume: 9
pages: 885-93
published year: 1996
authors:
  item: Nugent PG
  item: Albert A
  item: Orprayoon P
  item: Wilsher J
  item: Pitts JE
  item: Blundell TL
  item: Dhanaraj V

Mechanism of action of aspartic proteases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9561208
journal: Adv Exp Med Biol
volume: 436
pages: 115-21
published year: 1998
authors:
  item: Kashparov IV
  item: Popov ME
  item: Popov EM

Purification and crystallization of rhizopuspepsin: the use of nickel chelation chromatography to select for catalytically active species.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10419816
journal: Protein Expr Purif
volume: 16
pages: 213-20
published year: 1999
authors:
  item: Flentke GR
  item: Glinski J
  item: Satyshur K
  item: Rich DH

Free-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11783905
journal: Appl Biochem Biotechnol
volume: 96
pages: 93-108
published year: 2001
authors:
  item: Kalra P
  item: Das A
  item: Jayaram B

Design and synthesis of unsymmetrical peptidyl urea inhibitors of aspartic peptidases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11463304
journal: Org Lett
volume: 3
pages: 2313-6
published year: 2001
authors:
  item: Dales NA
  item: Bohacek RS
  item: Satyshur KA
  item: Rich DH

Aspartic protease inhibitors designed from computer-generated templates bind as predicted.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11463303
journal: Org Lett
volume: 3
pages: 2309-12
published year: 2001
authors:
  item: Ripka AS
  item: Satyshur KA
  item: Bohacek RS
  item: Rich DH

Effect of pH on the structure of rhizopuspepsin.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/14501114
journal: Acta Crystallogr D Biol Crystallogr
volume: 59
pages: 1755-61
published year: 2003
authors:
  item: Prasad BV
  item: Suguna K

TransitionStateAnalogue
compound: Amino-diol-tetrahedral intermediate
pdb: 4aprE01
ligand het code: PRO-PHE-HIS-STA-LEU (chain I)

TransitionStateAnalogue
compound: Amino-diol-tetrahedral intermediate
pdb: 5aprE01
ligand het code: PRO-PHE-CYS-STA-LEU-PHE-DHL (chain I)

TransitionStateAnalogue
compound: Amino-diol-tetrahedral intermediate
pdb: 6aprE01
ligand het code: IVA-VAL-VAL-STA-ALA-STA (chain I)

ReferenceForCatalyticMechanism
reference index: 5
reference section: Fig.5, p.7010-7012

ReferenceForCatalyticMechanism
reference index: 15
reference section: Fig.8, p.8139

ReferenceForCatalyticMechanism
reference index: 26
reference section: Fig.2, p.96-98