EzCatDB: D00440

DB codeD00440
RLCP classification1.13.200.966
CATH domainDomain 12.40.70.10Catalytic domain
Domain 22.40.70.10Catalytic domain
E.C.3.4.23.21
CSA2apr

CATH domainRelated DB codes (homologues)
2.40.70.10D00471,D00436,D00438,D00439,D00441,D00442,D00443,D00437,D00444,D00423,D00445,D00484,M00206,M00166,D00231,D00529

Enzyme Name
Swiss-protKEGG

P06026
Protein nameRhizopuspepsinrhizopuspepsin
Rhizopus aspartic proteinase
neurase
Rhizopus acid protease
Rhizopus acid proteinase
SynonymsEC 3.4.23.21


Swiss-prot:Accession NumberP06026
Entry nameCARP_RHICH
ActivityHydrolysis 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.
Subunit
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC00012C00017C00001C00012C00017I00136
CompoundPeptideProteinH2OPeptideProteinAmino-diol-tetrahedral intermediate
Typepeptide/proteinpeptide/proteinH2Opeptide/proteinpeptide/protein
2aprA01UnboundUnbound
UnboundUnboundUnbound
3aprE01Analogue:PRO-PHE-HIS-PUK-VAL-TYR(chain I)Unbound
UnboundUnboundUnbound
4aprE01UnboundUnbound
UnboundUnboundTransition-state-analogue:PRO-PHE-HIS-STA-LEU(chain I)
5aprE01UnboundUnbound
UnboundUnboundTransition-state-analogue:PRO-PHE-CYS-STA-LEU-PHE-DHL(chain I)
6aprE01UnboundUnbound
UnboundUnboundTransition-state-analogue:IVA-VAL-VAL-STA-ALA-STA(chain I)
2aprA02UnboundUnbound
UnboundUnboundUnbound
3aprE02UnboundUnbound
UnboundUnboundUnbound
4aprE02UnboundUnbound
UnboundUnboundUnbound
5aprE02UnboundUnbound
UnboundUnboundUnbound
6aprE02UnboundUnbound
UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P06026
pdbCatalytic residues
2aprA01ASP 35
3aprE01ASP 35
4aprE01ASP 35
5aprE01ASP 35
6aprE01ASP 35
2aprA02ASP 218
3aprE02ASP 218
4aprE02ASP 218
5aprE02ASP 218
6aprE02ASP 218

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]Fig.5, p.7010-7012
[15]Fig.8, p.8139
[26]Fig.2, p.96-98

references
[1]
PubMed ID596305
JournalAdv Exp Med Biol
Year1977
Volume95
Pages33-41
AuthorsSubramanian E, Liu M, Swan ID, Davies DR
TitleThe crystal structure of an acid protease from Rhizopus chinensis at 2.5 A resolution.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID77148881
PubMed ID322132
JournalProc Natl Acad Sci U S A
Year1977
Volume74
Pages556-9
AuthorsSubramanian E, Swan ID, Liu M, Davies DR, Jenkins JA, Tickle IJ, Blundell TL
TitleHomology among acid proteases: comparison of crystal structures at 3A resolution of acid proteases from Rhizopus chinensis and Endothia parasitica.
Related Swiss-protP06026
[3]
PubMed ID6309756
JournalJ Biochem (Tokyo)
Year1983
Volume93
Pages1297-304
AuthorsNakayama S, Nagashima Y, Hoshino M, Moriyama A, Takahashi K, Watanabe T, Yoshida M
TitleStructural study on the active site of porcine pepsin and Rhizopus chinensis acid protease. Spin labeling with diazoketone reagents.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID88062720
PubMed ID3316666
JournalJ Mol Biol
Year1987
Volume196
Pages877-900
AuthorsSuguna K, Bott RR, Padlan EA, Subramanian E, Sheriff S, Cohen GH, Davies DR
TitleStructure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
Related PDB2apr
Related Swiss-protP06026
[5]
CommentsX-ray crystallography
PubMed ID3313384
JournalProc Natl Acad Sci U S A
Year1987
Volume84
Pages7009-13
AuthorsSuguna K, Padlan EA, Smith CW, Carlson WD, Davies DR
TitleBinding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
Related PDB3apr
[6]
PubMed ID3284587
JournalBiochemistry
Year1988
Volume27
Pages1653-8
AuthorsGoldblum A
TitleTheoretical calculations on the acidity of the active site in aspartic proteinases.
[7]
PubMed ID2693742
JournalJ Mol Biol
Year1989
Volume210
Pages785-811
AuthorsSummers NL, Karplus M
TitleConstruction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.
[8]
PubMed ID2537531
JournalScience
Year1989
Volume243
Pages928-31
AuthorsWeber IT, Miller M, Jaskolski M, Leis J, Skalka AM, Wlodawer A
TitleMolecular modeling of the HIV-1 protease and its substrate binding site.
[9]
PubMed ID2201571
JournalFEBS Lett
Year1990
Volume269
Pages269-72
AuthorsGustchina A, Weber IT
TitleComparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap.
[10]
PubMed ID2115087
JournalJ Mol Biol
Year1990
Volume214
Pages143-70
AuthorsSielecki AR, Fedorov AA, Boodhoo A, Andreeva NS, James MN
TitleMolecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
[11]
PubMed ID2217165
JournalProteins
Year1990
Volume8
Pages62-81
AuthorsAbad-Zapatero C, Rydel TJ, Erickson J
TitleRevised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.
[12]
PubMed ID1742463
JournalBiophys J
Year1991
Volume60
Pages966-73
AuthorsMao B
TitleMass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor.
[13]
PubMed ID2050673
JournalJ Biol Chem
Year1991
Volume266
Pages11718-25
AuthorsChen Z, Koelsch G, Han HP, Wang XJ, Lin XL, Hartsuck JA, Tang J
TitleRecombinant rhizopuspepsinogen. Expression, purification, and activation properties of recombinant rhizopuspepsinogens.
[14]
PubMed ID1445256
JournalBiochem J
Year1992
Volume288
Pages109-16
AuthorsMao B
TitleMolecular-dynamics investigation of molecular flexibility in ligand binding.
[15]
PubMed ID1525154
JournalBiochemistry
Year1992
Volume31
Pages8125-41
AuthorsParris KD, Hoover DJ, Damon DB, Davies DR
TitleSynthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.
[16]
PubMed ID1526982
JournalJ Biol Chem
Year1992
Volume267
Pages18413-8
AuthorsLin Y, Fusek M, Lin X, Hartsuck JA, Kezdy FJ, Tang J
TitlepH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants.
[17]
CommentsX-ray crystallography
PubMed ID1603809
JournalProteins
Year1992
Volume13
Pages195-205
AuthorsSuguna K, Padlan EA, Bott R, Boger J, Parris KD, Davies DR
TitleStructures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
Related PDB4apr,5apr,6apr
[18]
PubMed ID1455175
JournalScand J Clin Lab Invest Suppl
Year1992
Volume210
Pages127-35
AuthorsTang J, Lin Y, Co E, Hartsuck JA, Lin X
TitleUnderstanding HIV protease: can it be translated into effective therapy against AIDS?
[19]
PubMed ID8215428
JournalArch Biochem Biophys
Year1993
Volume306
Pages297-303
AuthorsBalbaa M, Cunningham A, Hofmann T
TitleSecondary substrate binding in aspartic proteinases: contributions of subsites S3 and S'2 to kcat.
[20]
PubMed ID8196057
JournalJ Mol Biol
Year1994
Volume239
Pages249-75
AuthorsKoehl P, Delarue M
TitleApplication of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.
[21]
PubMed ID7854179
JournalMethods Enzymol
Year1994
Volume241
Pages195-224
AuthorsLin XL, Lin YZ, Tang J
TitleRelationships of human immunodeficiency virus protease with eukaryotic aspartic proteases.
[22]
PubMed ID7766059
JournalPhytochemistry
Year1995
Volume38
Pages27-30
AuthorsIchishima E, Ojima M, Yamagata Y, Hanzawa S, Nakamura T
TitleMolecular and enzymatic properties of an aspartic proteinase from Rhizopus hangchow.
[23]
PubMed ID8931128
JournalProtein Eng
Year1996
Volume9
Pages885-93
AuthorsNugent PG, Albert A, Orprayoon P, Wilsher J, Pitts JE, Blundell TL, Dhanaraj V
TitleProtein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop from rhizopuspepsin.
[24]
PubMed ID9561208
JournalAdv Exp Med Biol
Year1998
Volume436
Pages115-21
AuthorsKashparov IV, Popov ME, Popov EM
TitleMechanism of action of aspartic proteases.
[25]
PubMed ID10419816
JournalProtein Expr Purif
Year1999
Volume16
Pages213-20
AuthorsFlentke GR, Glinski J, Satyshur K, Rich DH
TitlePurification and crystallization of rhizopuspepsin: the use of nickel chelation chromatography to select for catalytically active species.
[26]
PubMed ID11783905
JournalAppl Biochem Biotechnol
Year2001
Volume96
Pages93-108
AuthorsKalra P, Das A, Jayaram B
TitleFree-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.
[27]
PubMed ID11463304
JournalOrg Lett
Year2001
Volume3
Pages2313-6
AuthorsDales NA, Bohacek RS, Satyshur KA, Rich DH
TitleDesign and synthesis of unsymmetrical peptidyl urea inhibitors of aspartic peptidases.
[28]
PubMed ID11463303
JournalOrg Lett
Year2001
Volume3
Pages2309-12
AuthorsRipka AS, Satyshur KA, Bohacek RS, Rich DH
TitleAspartic protease inhibitors designed from computer-generated templates bind as predicted.
[29]
PubMed ID14501114
JournalActa Crystallogr D Biol Crystallogr
Year2003
Volume59
Pages1755-61
AuthorsPrasad BV, Suguna K
TitleEffect of pH on the structure of rhizopuspepsin.

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.

createdupdated
2004-10-272012-06-28


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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