EzCatDB: D00512

DB codeD00512
RLCP classification1.13.11110.262
CATH domainDomain 13.30.70.340
Domain 23.40.630.10Catalytic domain
E.C.3.4.17.2

CATH domainRelated DB codes (homologues)
3.30.70.340D00193,D00467
3.40.630.10S00406,S00407,D00192,D00193,D00467

Enzyme Name
Swiss-protKEGG

P09955P15086
Protein nameCarboxypeptidase BCarboxypeptidase Bcarboxypeptidase B
protaminase
pancreatic carboxypeptidase B
tissue carboxypeptidase B
peptidyl-L-lysine [L-arginine]hydrolase
SynonymsEC 3.4.17.2
EC 3.4.17.2
Pancreas-specific protein
PASP


Swiss-prot:Accession NumberP09955P15086
Entry nameCBPB1_PIGCBPB1_HUMAN
ActivityPreferential release of a C-terminal lysine or arginine amino acid.Preferential release of a C-terminal lysine or arginine amino acid.
Subunit

Subcellular locationSecreted.Secreted.
CofactorBinds 1 zinc ion per subunit.Binds 1 zinc ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00038C00017C02188C00613C00001C00012C00047C00062
CompoundZincProteinProtein lysinePeptidyl-L-arginineH2OPeptideL-LysineL-Arginine
Typeheavy metalpeptide/proteinamine group,lipid,peptide/proteinamine group,imine group,peptide/proteinH2Opeptide/proteinamino acids,amine group,lipidamino acids,amine group,imine group,lipid
1nsaA01UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1pbaAUnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1kwmA02UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1kwmB02UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nsaA02Bound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1z5rABound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1z5rBBound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1z5rCBound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1zg7ABound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:P20
1zg7BBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:P20
1zg7CBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:P20
1zg8ABound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L98
1zg8BBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L98
1zg8CBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L98
1zg9ABound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L06
1zg9BBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L06
1zg9CBound:_ZNUnboundUnboundUnbound
UnboundUnboundAnalogue:L06
1kwmA01Bound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1kwmB01Bound:_ZNUnboundUnboundUnbound
UnboundUnboundUnbound
1zliABound:_ZNUnboundUnboundUnbound
Analogue:LEU 74(chainB)UnboundUnbound

Active-site residues
resource
literature [22]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1nsaA01


1pbaA


1kwmA02


1kwmB02


1nsaA02ARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1z5rAARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1z5rBARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1z5rCARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg7AARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg7BARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg7CARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg8AARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg8BARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg8CARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg9AARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg9BARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zg9CARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1kwmA01ARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1kwmB01ARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197
1zliAARG 127;GLU 270
HIS 69;GLU 72;HIS 196(Zinc binding)
SER 197

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.485-486
[11]p.3
[16]p.146-150
[17]p.383-384
[22]p.2381-2383
[28]p.285

references
[1]
PubMed ID7400116
JournalJ Biochem (Tokyo)
Year1980
Volume87
Pages1681-9
AuthorsKuroda K, Akanuma H, Sukenaga Y, Sugihara H, Yamasaki M
TitleLigand bindings of bovine carboxypeptidase B. III. Hydrophobic activators in dipeptide hydrolysis.
[2]
PubMed ID7390958
JournalJ Biochem (Tokyo)
Year1980
Volume87
Pages695-707
AuthorsSukenaga Y, Akanuma H, Suekane C, Yamasaki M
TitleLigand bindings of bovine carboxypeptidase B. II. Affinity chromatography and cooperative ligations.
[3]
PubMed ID7400117
JournalJ Biochem (Tokyo)
Year1980
Volume87
Pages1691-701
AuthorsSukenaga Y, Akanuma H, Yamasaki M
TitleLigand binding of bovine carboxypeptidase B. IV. Oligopeptide substrates and extended active center.
[4]
PubMed ID7118417
JournalInt J Pept Protein Res
Year1982
Volume19
Pages480-6
AuthorsZisapel N, Mallul Y, Sokolovsky M
TitleTyrosyl interactions at the active site of carboxypeptidase B.
[5]
PubMed ID6875538
JournalJ Inorg Biochem
Year1983
Volume18
Pages253-62
AuthorsZisapel N, Blank T, Sokolovsky M
TitleMetal ion effects on target sites of modification in metallocarboxypeptidase B.
[6]
PubMed ID3902502
JournalFEBS Lett
Year1985
Volume191
Pages273-7
AuthorsVilanova M, Burgos FJ, Cuchillo CM, Aviles FX
TitleUrea-gradient gel electrophoresis studies on the association of procarboxypeptidases A and B, proproteinase E, and their tryptic activation products.
[7]
PubMed ID3942789
JournalBiochim Biophys Acta
Year1986
Volume880
Pages171-8
AuthorsLipperheide C, Otto K
TitleImproved purification and some properties of bovine lysosomal carboxypeptidase B.
[8]
PubMed ID2920728
JournalEur J Biochem
Year1989
Volume179
Pages609-16
AuthorsPascual R, Burgos FJ, Salva M, Soriano F, Mendez E, Aviles FX
TitlePurification and properties of five different forms of human procarboxypeptidases.
[9]
CommentsSTRUCTURE BY NMR OF ACTIVATION PEPTIDE, AND SEQUENCE OF 1-81.
Medline ID91027767
PubMed ID2223783
JournalBiochemistry
Year1990
Volume29
Pages7515-22
AuthorsVendrell J, Wider G, Aviles FX, Wuthrich K
TitleSequence-specific 1H NMR assignments and determination of the secondary structure for the activation domain isolated from pancreatic procarboxypeptidase B.
Related Swiss-protP09955
[10]
PubMed ID2018774
JournalBiochemistry
Year1991
Volume30
Pages4082-9
AuthorsBurgos FJ, Salva M, Villegas V, Soriano F, Mendez E, Aviles FX
TitleAnalysis of the activation process of porcine procarboxypeptidase B and determination of the sequence of its activation segment.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID91114690
PubMed ID1989878
JournalEMBO J
Year1991
Volume10
Pages1-9
AuthorsColl M, Guasch A, Aviles FX, Huber R
TitleThree-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity.
Related PDB1nsa
Related Swiss-protP09955
[12]
CommentsSTRUCTURE BY NMR OF ACTIVATION PEPTIDE.
Medline ID91114693
PubMed ID1989879
JournalEMBO J
Year1991
Volume10
Pages11-5
AuthorsVendrell J, Billeter M, Wider G, Aviles FX, Wuthrich K
TitleThe NMR structure of the activation domain isolated from porcine procarboxypeptidase B.
Related PDB1pba
Related Swiss-protP09955
[13]
PubMed ID1915340
JournalEur J Biochem
Year1991
Volume200
Pages663-70
AuthorsConejero-Lara F, Sanchez-Ruiz JM, Mateo PL, Burgos FJ, Vendrell J, Aviles FX
TitleDifferential scanning calorimetric study of carboxypeptidase B, procarboxypeptidase B and its globular activation domain.
[14]
PubMed ID1515065
JournalBiol Chem Hoppe Seyler
Year1992
Volume373
Pages387-92
AuthorsVendrell J, Guasch A, Coll M, Villegas V, Billeter M, Wider G, Huber R, Wuthrich K, Aviles FX
TitlePancreatic procarboxypeptidases: their activation processes related to the structural features of the zymogens and activation segments.
[15]
CommentsSTRUCTURE BY NMR OF ACTIVATION PEPTIDE.
Medline ID93044373
PubMed ID1422143
JournalJ Biomol NMR
Year1992
Volume2
Pages1-10
AuthorsBilleter M, Vendrell J, Wider G, Aviles FX, Coll M, Guasch A, Huber R, Wuthrich K
TitleComparison of the NMR solution structure with the X-ray crystal structure of the activation domain from procarboxypeptidase B.
Related Swiss-protP09955
[16]
PubMed ID1548696
JournalJ Mol Biol
Year1992
Volume224
Pages141-57
AuthorsGuasch A, Coll M, Aviles FX, Huber R
TitleThree-dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation.
[17]
PubMed ID8436102
JournalEur J Biochem
Year1993
Volume211
Pages381-9
AuthorsAviles FX, Vendrell J, Guasch A, Coll M, Huber R
TitleAdvances in metallo-procarboxypeptidases. Emerging details on the inhibition mechanism and on the activation process.
[18]
PubMed ID8269943
JournalEur J Biochem
Year1993
Volume218
Pages529-34
AuthorsChan WW, Pfuetzner RA
TitleGeneral occurrence of binding synergism in zinc proteases and its possible significance.
[19]
PubMed ID8200353
JournalEur J Biochem
Year1994
Volume222
Pages55-63
AuthorsOppezzo O, Ventura S, Bergman T, Vendrell J, Jornvall H, Aviles FX
TitleProcarboxypeptidase in rat pancreas. Overall characterization and comparison of the activation processes.
[20]
PubMed ID7727441
JournalBiochemistry
Year1995
Volume34
Pages5811-6
AuthorsTan AK, Eaton DL
TitleActivation and characterization of procarboxypeptidase B from human plasma.
[21]
PubMed ID8528077
JournalProtein Sci
Year1995
Volume4
Pages1792-800
AuthorsVillegas V, Vendrell J, Aviles X
TitleThe activation pathway of procarboxypeptidase B from porcine pancreas: participation of the active enzyme in the proteolytic processing.
[22]
PubMed ID11848831
JournalChem Rev
Year1996
Volume96
Pages2375-2434
AuthorsLipscomb WN, Strater N
TitleRecent Advances in Zinc Enzymology.
[23]
PubMed ID9524066
JournalBiol Chem
Year1998
Volume379
Pages149-55
AuthorsAloy P, Catasus L, Villegas V, Reverter D, Vendrell J, Aviles FX
TitleComparative analysis of the sequences and three-dimensional models of human procarboxypeptidases A1, A2 and B.
[24]
PubMed ID9930672
JournalProtein Eng
Year1998
Volume11
Pages1229-34
AuthorsEdge M, Forder C, Hennam J, Lee I, Tonge D, Hardern I, Fitton J, Eckersley K, East S, Shufflebotham A, Blakey D, Slater A
TitleEngineered human carboxypeptidase B enzymes that hydrolyse hippuryl-L-glutamic acid: reversed-polarity mutants.
[25]
PubMed ID9862207
JournalProtein Eng
Year1998
Volume11
Pages881-90
AuthorsMarti-Renom MA, Mas JM, Oliva B, Querol E, Aviles FX
TitleEffects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B.
[26]
PubMed ID10021925
JournalBioorg Med Chem Lett
Year1999
Volume9
Pages187-92
AuthorsMock WL, Xu D
TitleCatalytic activity of carboxypeptidase B and of carboxypeptidase Y with anisylazoformyl substrates.
[27]
PubMed ID10391940
JournalJ Biol Chem
Year1999
Volume274
Pages19925-33
AuthorsVentura S, Villegas V, Sterner J, Larson J, Vendrell J, Hershberger CL, Aviles FX
TitleMapping the pro-region of carboxypeptidase B by protein engineering. Cloning, overexpression, and mutagenesis of the porcine proenzyme.
[28]
PubMed ID10708864
JournalBiochim Biophys Acta
Year2000
Volume1477
Pages284-98
AuthorsVendrell J, Querol E, Aviles FX
TitleMetallocarboxypeptidases and their protein inhibitors. Structure, function and biomedical properties.
[29]
PubMed ID10679526
JournalProtein Eng
Year2000
Volume13
Pages21-6
AuthorsGargallo R, Oliva B, Querol E, Aviles FX
TitleEffect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B.
[30]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 16-417.
PubMed ID12162965
JournalJ Mol Biol
Year2002
Volume321
Pages537-47
AuthorsBarbosa Pereira PJ, Segura-Martin S, Oliva B, Ferrer-Orta C, Aviles FX, Coll M, Gomis-Ruth FX, Vendrell J
TitleHuman procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI).
Related PDB1kwm
Related Swiss-protP15086
[31]
CommentsX-ray Diffraction
PubMed ID15982000
JournalBiochemistry
Year2005
Volume44
Pages9339-47
AuthorsAdler M, Bryant J, Buckman B, Islam I, Larsen B, Finster S, Kent L, May K, Mohan R, Yuan S, Whitlow M
TitleCrystal structures of potent thiol-based inhibitors bound to carboxypeptidase B.
Related PDB1z5r,1zg7,1zg8,1zg9
[32]
CommentsX-ray Diffraction
PubMed ID15961103
JournalJ Mol Biol
Year2005
Volume350
Pages489-98
AuthorsArolas JL, Popowicz GM, Lorenzo J, Sommerhoff CP, Huber R, Aviles FX, Holak TA
TitleThe three-dimensional structures of tick carboxypeptidase inhibitor in complex with A/B carboxypeptidases reveal a novel double-headed binding mode.
Related PDB1zli

comments
This enzyme belongs to the peptidase family-M14.
Moreover, this enzyme is homologous to carboxypeptidase A (E.C. 3.4.17.1; D00467 in EzCatDB), carboxypeptidase T (E.C. 3.4.17.18; S00407) and carboxypeptidase A2 (E.C. 3.4.17.15; D00193) with conserved catalytic residues. Thus, they might have the same catalytic mechanism.
According to the literature [22], the catalytic reaction proceeds as follows:
(1) Glu270 acts as a general base to activate the hydrolytic water, along with the Zinc ion bound to His69/Glu72/His196.
(2) The activated water makes a nucleophilic attack on the target carbonyl carbon, whilst Arg127 is hydrogen bonded to the carbonyl oxygen, facilitating the formation of the tetrahedral (or gem-diolate) transition-state.
(3) The transition-state is stabilized by both Zinc ion and Arg127, along with the mainchain carbonyl of Ser197 and the sidechain oxygen of Glu270.
(4) Glu270 acts as a general acid to protonate the leaving amine group, completing the hydrolysis.

createdupdated
2004-07-062009-02-26
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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