EzCatDB: D00436
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DB codeD00436
RLCP classification1.13.200.966 : Hydrolysis
CATH domainDomain 12.40.70.10 : Cathepsin D, subunit A; domain 1Catalytic domain
Domain 22.40.70.10 : Cathepsin D, subunit A; domain 1Catalytic domain
E.C.3.4.23.1

CATH domainRelated DB codes (homologues)
2.40.70.10 : Cathepsin D, subunit A; domain 1D00471,D00438,D00439,D00440,D00441,D00442,D00443,D00437,D00444,D00423,D00445,D00484,M00206,M00166,D00231,D00529

Enzyme Name
UniProtKBKEGG

P00791P0DJD9
Protein namePepsin A
pepsin A
pepsin
lactated pepsin
pepsin fortior
fundus-pepsin
elixir lactate of pepsin
P I
lactated pepsin elixir
P II
pepsin R
pepsin D
SynonymsEC 3.4.23.1
None
RefSeq
NP_055039.1 (Protein)
NM_014224.2 (DNA/RNA sequence)
MEROPSA01.001 (Aspartic)
A01.071 (Aspartic)
PfamPF07966 (A1_Propeptide)
PF00026 (Asp)
[Graphical view]
PF07966 (A1_Propeptide)
PF00026 (Asp)
[Graphical view]


UniProtKB:Accession NumberP00791P0DJD9
Entry namePEPA_PIGPEPA5_HUMAN
ActivityPreferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1'' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin.Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin.
Subunit

Subcellular locationSecreted.Secreted.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00012C00017C00001C00012C00017I00136
CompoundPeptideProteinH2OPeptideProteinAmino-diol-tetrahedral intermediate
Typepeptide/proteinpeptide/proteinH2Opeptide/proteinpeptide/protein
ChEBI

15377



PubChem

962
22247451



              
1f34A01UnboundUnbound UnboundUnboundUnbound
1psaA01Analogue:0ZLUnbound UnboundUnboundUnbound
1psaB01Analogue:0ZLUnbound UnboundUnboundUnbound
1yx9A01UnboundUnbound UnboundUnboundUnbound
2psgA01UnboundUnbound UnboundUnboundUnbound
3pepA01UnboundUnbound UnboundUnboundUnbound
3psgA01UnboundUnbound UnboundUnboundUnbound
4pepA01UnboundUnbound UnboundUnboundUnbound
5pepA01UnboundUnbound UnboundUnboundUnbound
1flhA01UnboundUnbound UnboundUnboundUnbound
1psnA01UnboundUnbound UnboundUnboundUnbound
1psoE01Analogue:IVA-VAL-VAL-STA-ALA-STA(chain I)Unbound UnboundUnboundUnbound
1qrpE01UnboundUnbound UnboundUnboundTransition-state-analogue:HH0
3utlA01UnboundUnbound UnboundUnboundUnbound
1f34A02UnboundUnbound UnboundBound:GLN 1(chain B)Unbound
1psaA02UnboundUnbound UnboundUnboundUnbound
1psaB02UnboundUnbound UnboundUnboundUnbound
1yx9A02UnboundUnbound UnboundUnboundUnbound
2psgA02UnboundUnbound UnboundUnboundUnbound
3pepA02UnboundUnbound UnboundUnboundUnbound
3psgA02UnboundUnbound UnboundUnboundUnbound
4pepA02UnboundUnbound UnboundUnboundUnbound
5pepA02UnboundUnbound UnboundUnboundUnbound
1flhA02UnboundUnbound UnboundUnboundUnbound
1psnA02UnboundUnbound UnboundUnboundUnbound
1psoE02UnboundUnbound UnboundUnboundUnbound
1qrpE02UnboundUnbound UnboundUnboundUnbound
3utlA02UnboundUnbound UnboundUnboundUnbound

Active-site residues
pdbCatalytic residues
         
1f34A01ASP 32
1psaA01ASP 32
1psaB01ASP 32
1yx9A01ASP 32
2psgA01ASP 32
3pepA01ASP 32
3psgA01ASP 32
4pepA01ASP 32
5pepA01ASP 32
1flhA01ASP 32
1psnA01ASP 32
1psoE01ASP 32
1qrpE01ASP 32
3utlA01ASP 32
1f34A02ASP 215
1psaA02ASP 215
1psaB02ASP 215
1yx9A02ASP 215
2psgA02ASP 215
3pepA02ASP 215
3psgA02ASP 215
4pepA02ASP 215
5pepA02ASP 215
1flhA02ASP 215
1psnA02ASP 215
1psoE02ASP 215
1qrpE02ASP 215
3utlA02ASP 215

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[10]Fig.5, p.7010-70123
[23]p.18414-18417
[25]Fig.5, p.3331-33323
[41]p.276-278
[46]Fig.6

references
[1]
CommentsACTIVE SITE.
Medline ID69283592
PubMed ID4897201
JournalBiochem J
Year1969
Volume113
Pages377-86
AuthorsBayliss RS, Knowles JR, Wybrandt GB
TitleAn aspartic acid residue at the active site of pepsin. The isolation and sequence of the heptapeptide.
Related UniProtKBP00791
[2]
PubMed ID4940603
JournalArch Biochem Biophys
Year1971
Volume144
Pages59-65
AuthorsNakagawa Y, Perlmann GE
TitleDisulfide bonds of pepsinogen and pepsin: identification of the disulfide bonds which can be reversibly reduced and reoxidized.
[3]
PubMed ID4946266
JournalBiochem Biophys Res Commun
Year1971
Volume45
Pages293-6
AuthorsHubbard CD, Stein TP
TitleThe pepsin catalysed hydrolysis of bis-P-nitrophenyl sulfite.
[4]
PubMed ID4561920
JournalBiochem J
Year1972
Volume127
Pages35P
AuthorsTakahashi M, Hofmann T
TitleEvidence for an acyl intermediate in pepsin-catalysed reactions.
[5]
PubMed ID782445
JournalBiochem J
Year1976
Volume153
Pages691-9
AuthorsWang TT, Hofmann T
TitleAcyl and amino intermediates in reactions catalysed by pig pepsin. Analysis of transpeptidation products.
[6]
CommentsX-RAY CRYSTALLOGRAPHY.
Medline ID78077917
PubMed ID339692
JournalAdv Exp Med Biol
Year1977
Volume95
Pages23-31
AuthorsAndreeva NS, Gustchina AE, Fedorov AA, Shutzkever NE, Volnova TV
TitleX-ray crystallographic studies of pepsin.
Related UniProtKBP00791
[7]
PubMed ID346376
JournalFEBS Lett
Year1978
Volume88
Pages87-90
AuthorsAntonov VK, Ginodman LM, Kapitannikov YV, Barshevskaya TN, Gurova AG, Rumsh LD
TitleMechanism of pepsin catalysis: general base catalysis by the active-site carboxylate ion.
[8]
PubMed ID2862261
JournalJ Pharm Pharmacol
Year1985
Volume37
Pages396-400
AuthorsLawton JB, Mekas CI
TitleThe effect of polycations on the activity of pepsin.
[9]
PubMed ID3109484
JournalBiochim Biophys Acta
Year1987
Volume913
Pages122-30
AuthorsDunn BM, Valler MJ, Rolph CE, Foundling SI, Jimenez M, Kay J
TitleThe pH dependence of the hydrolysis of chromogenic substrates of the type, Lys-Pro-Xaa-Yaa-Phe-(NO2)Phe-Arg-Leu, by selected aspartic proteinases: evidence for specific interactions in subsites S3 and S2.
[10]
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.
[11]
PubMed ID2492190
JournalBiochem Biophys Res Commun
Year1989
Volume158
Pages115-9
AuthorsMcPhie P
TitleA reversible unfolding reaction of swine pepsin; implications for pepsinogen's folding mechanism.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID90317821
PubMed ID2115088
JournalJ Mol Biol
Year1990
Volume214
Pages199-222
AuthorsCooper JB, Khan G, Taylor G, Tickle IJ, Blundell TL
TitleX-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution.
Related PDB5pep
Related UniProtKBP00791
[13]
CommentsX-ray crystallography
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.
Related PDB4pep
[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID91017500
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.
Related PDB3pep
Related UniProtKBP00791
[15]
PubMed ID1812734
JournalAdv Exp Med Biol
Year1991
Volume306
Pages39-45
AuthorsAndreeva NS, James MN
TitleWhy does pepsin have a negative charge at very low pH? An analysis of conserved charged residues in aspartic proteinases.
[16]
PubMed ID2065096
JournalBiochim Biophys Acta
Year1991
Volume1078
Pages283-8
AuthorsMakarov AA, Protasevich II, Frank EG, Grishina IB, Bolotina IA, Esipova NG
TitleThe number of cooperative regions (energetic domains) in a pepsin molecule depends on the pH of the medium.
[17]
PubMed ID1820069
JournalBiomed Biochim Acta
Year1991
Volume50
PagesS94-7
AuthorsBemquerer MP, Theobaldo FC, Tominaga M
TitlePepsin-catalyzed peptide synthesis in biphasic systems.
[18]
PubMed ID1820070
JournalBiomed Biochim Acta
Year1991
Volume50
PagesS98-101
AuthorsFilippova IYu, Lysogorskaya EN, Anisimova VV, Abdel Malak CA, Lavrenova GI, Stepanov VM
TitlePepsin behavior as a catalyst in equilibrium-controlled peptide synthesis.
[19]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID91278095
PubMed ID2056534
JournalJ Mol Biol
Year1991
Volume219
Pages671-92
AuthorsSielecki AR, Fujinaga M, Read RJ, James MN
TitleRefined structure of porcine pepsinogen at 1.8 A resolution.
Related PDB2psg
Related UniProtKBP00791
[20]
CommentsX-ray crystallography
PubMed ID1418819
JournalActa Crystallogr B
Year1992
Volume48
Pages476-88
AuthorsChen L, Erickson JW, Rydel TJ, Park CH, Neidhart D, Luly J, Abad-Zapatero C
TitleStructure of a pepsin/renin inhibitor complex reveals a novel crystal packing induced by minor chemical alterations in the inhibitor.
Related PDB1psa
[21]
PubMed ID1428533
JournalInt J Pept Protein Res
Year1992
Volume39
Pages443-9
AuthorsAbdel Malak C, Filippova IY, Lysogorskaya EN, Anisimova VV, Lavrenova GI, Stepanov VM
TitlePepsin as a catalyst of peptide synthesis. Enzyme co-precipitation with emerging peptide products.
[22]
PubMed ID1512263
JournalJ Biol Chem
Year1992
Volume267
Pages17257-63
AuthorsLin XL, Lin YZ, Koelsch G, Gustchina A, Wlodawer A, Tang J
TitleEnzymic activities of two-chain pepsinogen, two-chain pepsin, and the amino-terminal lobe of pepsinogen.
[23]
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.
[24]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID92279205
PubMed ID1594574
JournalProteins
Year1992
Volume13
Pages1-25
AuthorsHartsuck JA, Koelsch G, Remington SJ
TitleThe high-resolution crystal structure of porcine pepsinogen.
Related PDB3psg
Related UniProtKBP00791
[25]
PubMed ID8461297
JournalBiochemistry
Year1993
Volume32
Pages3325-33
AuthorsBeveridge AJ, Heywood GC
TitleA quantum mechanical study of the active site of aspartic proteinases.
[26]
PubMed ID8401224
JournalProtein Sci
Year1993
Volume2
Pages1383-90
AuthorsLin X, Loy JA, Sussman F, Tang J
TitleConformational instability of the N- and C-terminal lobes of porcine pepsin in neutral and alkaline solutions.
[27]
PubMed ID7925992
JournalFEBS Lett
Year1994
Volume352
Pages315-7
AuthorsIliadis G, Zundel G, Brzezinski B
TitleAspartic proteinases--Fourier transform IR studies of the aspartic carboxylic groups in the active site of pepsin.
[28]
PubMed ID8138045
JournalInt J Biochem
Year1994
Volume26
Pages35-42
AuthorsBalbaa M, Blum M, Hofmann T
TitleMechanism of pepsin-catalyzed aminotranspeptidation reactions.
[29]
PubMed ID7896503
JournalInt J Pept Protein Res
Year1994
Volume44
Pages448-56
AuthorsBemquerer MP, Adlercreutz P, Tominaga M
TitlePepsin-catalyzed peptide synthesis in organic media: studies with free and immobilized enzyme.
[30]
PubMed ID8540318
JournalAdv Exp Med Biol
Year1995
Volume362
Pages19-32
AuthorsAndreeva NS, Bochkarev A, Pechik I
TitleA new way of looking at aspartic proteinase structures: a comparison of pepsin structure to other aspartic proteinases in the near active site region.
[31]
PubMed ID8540385
JournalAdv Exp Med Biol
Year1995
Volume362
Pages91-4
AuthorsRao C, Dunn BM
TitleEvidence for electrostatic interactions in the S2 subsite of porcine pepsin.
[32]
PubMed ID8556555
JournalClin Exp Allergy
Year1995
Volume25
Pages1007-17
AuthorsSchmidt DG, Meijer RJ, Slangen CJ, van Beresteijn EC
TitleRaising the pH of the pepsin-catalysed hydrolysis of bovine whey proteins increases the antigenicity of the hydrolysates.
[33]
PubMed ID7650014
JournalJ Biol Chem
Year1995
Volume270
Pages19974-8
AuthorsCottrell TJ, Harris LJ, Tanaka T, Yada RY
TitleThe sole lysine residue in porcine pepsin works as a key residue for catalysis and conformational flexibility.
[34]
PubMed ID7593830
JournalJ Dairy Res
Year1995
Volume62
Pages451-67
AuthorsPlowman JE, Creamer LK
TitleRestrained molecular dynamics study of the interaction between bovine kappa-casein peptide 98-111 and bovine chymosin and porcine pepsin.
[35]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID95392399
PubMed ID7663352
JournalProtein Sci
Year1995
Volume4
Pages960-72
AuthorsFujinaga M, Chernaia MM, Tarasova NI, Mosimann SC, James MN
TitleCrystal structure of human pepsin and its complex with pepstatin.
Related PDB1psn,1pso
Related UniProtKBP00790
[36]
PubMed ID8907496
JournalInt J Pept Protein Res
Year1996
Volume47
Pages28-35
AuthorsAnisimova VV, Filippova IY, Lysogorskaya EN, Oksenoit ES, Kolobanova SV, Stepanov VM
TitleProteinase-catalyzed peptide synthesis in concentrated solutions of urea and other denaturing agents.
[37]
PubMed ID9228062
JournalJ Biol Chem
Year1997
Volume272
Pages18855-61
AuthorsShintani T, Nomura K, Ichishima E
TitleEngineering of porcine pepsin. Alteration of S1 substrate specificity of pepsin to those of fungal aspartic proteinases by site-directed mutagenesis.
[38]
CommentsX-ray crystallography
PubMed ID9761815
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages32-46
AuthorsKarlsen S, Hough E, Olsen RL
TitleStructure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua).
Related PDB1am5
[39]
PubMed ID10408333
JournalJ Pept Res
Year1999
Volume53
Pages606-10
AuthorsMalak CA
TitlePepsin as a catalyst for peptide synthesis: formation of peptide bonds not typical for pepsin substrate specificity.
[40]
PubMed ID10065711
JournalProtein Eng
Year1999
Volume12
Pages55-61
AuthorsOkoniewska M, Tanaka T, Yada RY
TitleThe role of the flap residue, threonine 77, in the activation and catalytic activity of pepsin A.
[41]
CommentsX-ray crystallography
PubMed ID10713513
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages272-9
AuthorsFujinaga M, Cherney MM, Tarasova NI, Bartlett PA, Hanson JE, James MN
TitleStructural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.
Related PDB1qrp
[42]
PubMed ID10861225
JournalBiochem J
Year2000
Volume349
Pages169-77
AuthorsOkoniewska M, Tanaka T, Yada RY
TitleThe pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis.
[43]
CommentsX-ray crystallography
PubMed ID10932249
JournalNat Struct Biol
Year2000
Volume7
Pages653-7
AuthorsNg KK, Petersen JF, Cherney MM, Garen C, Zalatoris JJ, Rao-Naik C, Dunn BM, Martzen MR, Peanasky RJ, James MN
TitleStructural basis for the inhibition of porcine pepsin by Ascaris pepsin inhibitor-3.
Related PDB1f34
[44]
CommentsX-ray crystallography
PubMed ID11679720
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1560-70
AuthorsCanduri F, Teodoro LG, Fadel V, Lorenzi CC, Hial V, Gomes RA, Neto JR, de Azevedo WF Jr
TitleStructure of human uropepsin at 2.45 A resolution.
Related PDB1flh
[45]
PubMed ID11707613
JournalProtein Eng
Year2001
Volume14
Pages669-74
AuthorsTanaka T, Yada RY
TitleN-terminal portion acts as an initiator of the inactivation of pepsin at neutral pH.
[46]
PubMed ID11714911
JournalProtein Sci
Year2001
Volume10
Pages2439-50
AuthorsAndreeva NS, Rumsh LD
TitleAnalysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes.
[47]
PubMed ID12089768
JournalQ Rev Biol
Year2002
Volume77
Pages127-47
AuthorsFruton JS
TitleA history of pepsin and related enzymes.
[48]
PubMed ID15883044
JournalBiochem Biophys Res Commun
Year2005
Volume331
Pages1510-4
AuthorsKesavulu MM, Ramasubramanian S, Suguna K
TitleEffect of dimethyl sulphoxide on the crystal structure of porcine pepsin.
Related PDB1yx9
[49]
PubMed ID22525752
JournalActa Crystallogr D Biol Crystallogr
Year2012
Volume68
Pages541-52
AuthorsBailey D, Carpenter EP, Coker A, Coker S, Read J, Jones AT, Erskine P, Aguilar CF, Badasso M, Toldo L, Rippmann F, Sanz-Aparicio J, Albert A, Blundell TL, Roberts NB, Wood SP, Cooper JB
TitleAn analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases.
Related PDB3utl

comments
This enzyme belongs to the peptidase family-A1.
According to the literature [10], [25] & [41], the catalytic reaction proceeds as follows:
(1) Asp215 acts as a general base, abstracting a proton from a water molecule, which is bound between Asp32 and Asp215.
(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 Asp32 stabilzes the negative charge of the transition state.
(4) Asp215 acts as a general acid, protonating to the leaving amine group. This step leads to the cleavage of the peptide bond.

createdupdated
2004-10-142012-06-27


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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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