DB code: D00512

RLCP classification 1.13.11110.262 : Hydrolysis
CATH domain 3.30.70.340 : Alpha-Beta Plaits
3.40.630.10 : Aminopeptidase Catalytic domain
E.C. 3.4.17.2
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.630.10 : Aminopeptidase S00406 S00407 D00192 D00193 D00467
3.30.70.340 : Alpha-Beta Plaits D00193 D00467

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq MEROPS Pfam
P09955 Carboxypeptidase B
EC 3.4.17.2
NP_999334.1 (Protein)
NM_214169.1 (DNA/RNA sequence)
M14.003 (Metallo)
PF00246 (Peptidase_M14)
PF02244 (Propep_M14)
[Graphical View]
P15086 Carboxypeptidase B
EC 3.4.17.2
Pancreas-specific protein
PASP
NP_001862.2 (Protein)
NM_001871.2 (DNA/RNA sequence)
M14.003 (Metallo)
PF00246 (Peptidase_M14)
PF02244 (Propep_M14)
[Graphical View]

KEGG enzyme name
carboxypeptidase B
protaminase
pancreatic carboxypeptidase B
tissue carboxypeptidase B
peptidyl-L-lysine [L-arginine]hydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P09955 CBPB1_PIG Preferential release of a C-terminal lysine or arginine amino acid. Secreted. Binds 1 zinc ion per subunit.
P15086 CBPB1_HUMAN Preferential release of a C-terminal lysine or arginine amino acid. Secreted. Binds 1 zinc ion per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00017 C02188 C00613 C00001 C00012 C00047 C00062
E.C.
Compound Zinc Protein Protein lysine Peptidyl-L-arginine H2O Peptide L-Lysine L-Arginine
Type heavy metal peptide/protein amine group,lipid,peptide/protein amine group,imine group,peptide/protein H2O peptide/protein amino acids,amine group,lipid amino acids,amine group,imine group,lipid
ChEBI 29105
15377
18019
16467
PubChem 32051
22247451
962
5962
71774817
28782
6322
1nsaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1pbaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kwmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kwmB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nsaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1z5rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1z5rB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1z5rC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1zg7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:P20
1zg7B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:P20
1zg7C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:P20
1zg8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L98
1zg8B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L98
1zg8C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L98
1zg9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L06
1zg9B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L06
1zg9C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Analogue:L06
1kwmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1kwmB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound
1zliA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Analogue:LEU_74 (chainB) Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [22]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1nsaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1pbaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kwmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kwmB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nsaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1z5rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1z5rB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1z5rC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg7B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg7C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg8B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg8C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg9B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zg9C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1kwmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1kwmB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197
1zliA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 127;GLU 270 HIS 69;GLU 72;HIS 196(Zinc binding) SER 197

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 7400116
Journal J Biochem (Tokyo)
Year 1980
Volume 87
Pages 1681-9
Authors Kuroda K, Akanuma H, Sukenaga Y, Sugihara H, Yamasaki M
Title Ligand bindings of bovine carboxypeptidase B. III. Hydrophobic activators in dipeptide hydrolysis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7390958
Journal J Biochem (Tokyo)
Year 1980
Volume 87
Pages 695-707
Authors Sukenaga Y, Akanuma H, Suekane C, Yamasaki M
Title Ligand bindings of bovine carboxypeptidase B. II. Affinity chromatography and cooperative ligations.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7400117
Journal J Biochem (Tokyo)
Year 1980
Volume 87
Pages 1691-701
Authors Sukenaga Y, Akanuma H, Yamasaki M
Title Ligand binding of bovine carboxypeptidase B. IV. Oligopeptide substrates and extended active center.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7118417
Journal Int J Pept Protein Res
Year 1982
Volume 19
Pages 480-6
Authors Zisapel N, Mallul Y, Sokolovsky M
Title Tyrosyl interactions at the active site of carboxypeptidase B.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 6875538
Journal J Inorg Biochem
Year 1983
Volume 18
Pages 253-62
Authors Zisapel N, Blank T, Sokolovsky M
Title Metal ion effects on target sites of modification in metallocarboxypeptidase B.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3902502
Journal FEBS Lett
Year 1985
Volume 191
Pages 273-7
Authors Vilanova M, Burgos FJ, Cuchillo CM, Aviles FX
Title Urea-gradient gel electrophoresis studies on the association of procarboxypeptidases A and B, proproteinase E, and their tryptic activation products.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 3942789
Journal Biochim Biophys Acta
Year 1986
Volume 880
Pages 171-8
Authors Lipperheide C, Otto K
Title Improved purification and some properties of bovine lysosomal carboxypeptidase B.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 2920728
Journal Eur J Biochem
Year 1989
Volume 179
Pages 609-16
Authors Pascual R, Burgos FJ, Salva M, Soriano F, Mendez E, Aviles FX
Title Purification and properties of five different forms of human procarboxypeptidases.
Related PDB
Related UniProtKB
[9]
Resource
Comments STRUCTURE BY NMR OF ACTIVATION PEPTIDE, AND SEQUENCE OF 1-81.
Medline ID 91027767
PubMed ID 2223783
Journal Biochemistry
Year 1990
Volume 29
Pages 7515-22
Authors Vendrell J, Wider G, Aviles FX, Wuthrich K
Title Sequence-specific 1H NMR assignments and determination of the secondary structure for the activation domain isolated from pancreatic procarboxypeptidase B.
Related PDB
Related UniProtKB P09955
[10]
Resource
Comments
Medline ID
PubMed ID 2018774
Journal Biochemistry
Year 1991
Volume 30
Pages 4082-9
Authors Burgos FJ, Salva M, Villegas V, Soriano F, Mendez E, Aviles FX
Title Analysis of the activation process of porcine procarboxypeptidase B and determination of the sequence of its activation segment.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 91114690
PubMed ID 1989878
Journal EMBO J
Year 1991
Volume 10
Pages 1-9
Authors Coll M, Guasch A, Aviles FX, Huber R
Title Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity.
Related PDB 1nsa
Related UniProtKB P09955
[12]
Resource
Comments STRUCTURE BY NMR OF ACTIVATION PEPTIDE.
Medline ID 91114693
PubMed ID 1989879
Journal EMBO J
Year 1991
Volume 10
Pages 11-5
Authors Vendrell J, Billeter M, Wider G, Aviles FX, Wuthrich K
Title The NMR structure of the activation domain isolated from porcine procarboxypeptidase B.
Related PDB 1pba
Related UniProtKB P09955
[13]
Resource
Comments
Medline ID
PubMed ID 1915340
Journal Eur J Biochem
Year 1991
Volume 200
Pages 663-70
Authors Conejero-Lara F, Sanchez-Ruiz JM, Mateo PL, Burgos FJ, Vendrell J, Aviles FX
Title Differential scanning calorimetric study of carboxypeptidase B, procarboxypeptidase B and its globular activation domain.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 1515065
Journal Biol Chem Hoppe Seyler
Year 1992
Volume 373
Pages 387-92
Authors Vendrell J, Guasch A, Coll M, Villegas V, Billeter M, Wider G, Huber R, Wuthrich K, Aviles FX
Title Pancreatic procarboxypeptidases: their activation processes related to the structural features of the zymogens and activation segments.
Related PDB
Related UniProtKB
[15]
Resource
Comments STRUCTURE BY NMR OF ACTIVATION PEPTIDE.
Medline ID 93044373
PubMed ID 1422143
Journal J Biomol NMR
Year 1992
Volume 2
Pages 1-10
Authors Billeter M, Vendrell J, Wider G, Aviles FX, Coll M, Guasch A, Huber R, Wuthrich K
Title Comparison of the NMR solution structure with the X-ray crystal structure of the activation domain from procarboxypeptidase B.
Related PDB
Related UniProtKB P09955
[16]
Resource
Comments
Medline ID
PubMed ID 1548696
Journal J Mol Biol
Year 1992
Volume 224
Pages 141-57
Authors Guasch A, Coll M, Aviles FX, Huber R
Title Three-dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 8436102
Journal Eur J Biochem
Year 1993
Volume 211
Pages 381-9
Authors Aviles FX, Vendrell J, Guasch A, Coll M, Huber R
Title Advances in metallo-procarboxypeptidases. Emerging details on the inhibition mechanism and on the activation process.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 8269943
Journal Eur J Biochem
Year 1993
Volume 218
Pages 529-34
Authors Chan WW, Pfuetzner RA
Title General occurrence of binding synergism in zinc proteases and its possible significance.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 8200353
Journal Eur J Biochem
Year 1994
Volume 222
Pages 55-63
Authors Oppezzo O, Ventura S, Bergman T, Vendrell J, Jornvall H, Aviles FX
Title Procarboxypeptidase in rat pancreas. Overall characterization and comparison of the activation processes.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 7727441
Journal Biochemistry
Year 1995
Volume 34
Pages 5811-6
Authors Tan AK, Eaton DL
Title Activation and characterization of procarboxypeptidase B from human plasma.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 8528077
Journal Protein Sci
Year 1995
Volume 4
Pages 1792-800
Authors Villegas V, Vendrell J, Aviles X
Title The activation pathway of procarboxypeptidase B from porcine pancreas: participation of the active enzyme in the proteolytic processing.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11848831
Journal Chem Rev
Year 1996
Volume 96
Pages 2375-2434
Authors Lipscomb WN, Strater N
Title Recent Advances in Zinc Enzymology.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 9524066
Journal Biol Chem
Year 1998
Volume 379
Pages 149-55
Authors Aloy P, Catasus L, Villegas V, Reverter D, Vendrell J, Aviles FX
Title Comparative analysis of the sequences and three-dimensional models of human procarboxypeptidases A1, A2 and B.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 9930672
Journal Protein Eng
Year 1998
Volume 11
Pages 1229-34
Authors Edge M, Forder C, Hennam J, Lee I, Tonge D, Hardern I, Fitton J, Eckersley K, East S, Shufflebotham A, Blakey D, Slater A
Title Engineered human carboxypeptidase B enzymes that hydrolyse hippuryl-L-glutamic acid: reversed-polarity mutants.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 9862207
Journal Protein Eng
Year 1998
Volume 11
Pages 881-90
Authors Marti-Renom MA, Mas JM, Oliva B, Querol E, Aviles FX
Title Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 10021925
Journal Bioorg Med Chem Lett
Year 1999
Volume 9
Pages 187-92
Authors Mock WL, Xu D
Title Catalytic activity of carboxypeptidase B and of carboxypeptidase Y with anisylazoformyl substrates.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 10391940
Journal J Biol Chem
Year 1999
Volume 274
Pages 19925-33
Authors Ventura S, Villegas V, Sterner J, Larson J, Vendrell J, Hershberger CL, Aviles FX
Title Mapping the pro-region of carboxypeptidase B by protein engineering. Cloning, overexpression, and mutagenesis of the porcine proenzyme.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 10708864
Journal Biochim Biophys Acta
Year 2000
Volume 1477
Pages 284-98
Authors Vendrell J, Querol E, Aviles FX
Title Metallocarboxypeptidases and their protein inhibitors. Structure, function and biomedical properties.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 10679526
Journal Protein Eng
Year 2000
Volume 13
Pages 21-6
Authors Gargallo R, Oliva B, Querol E, Aviles FX
Title Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B.
Related PDB
Related UniProtKB
[30]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 16-417.
Medline ID
PubMed ID 12162965
Journal J Mol Biol
Year 2002
Volume 321
Pages 537-47
Authors Barbosa Pereira PJ, Segura-Martin S, Oliva B, Ferrer-Orta C, Aviles FX, Coll M, Gomis-Ruth FX, Vendrell J
Title Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI).
Related PDB 1kwm
Related UniProtKB P15086
[31]
Resource
Comments X-ray Diffraction
Medline ID
PubMed ID 15982000
Journal Biochemistry
Year 2005
Volume 44
Pages 9339-47
Authors Adler M, Bryant J, Buckman B, Islam I, Larsen B, Finster S, Kent L, May K, Mohan R, Yuan S, Whitlow M
Title Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase B.
Related PDB 1z5r 1zg7 1zg8 1zg9
Related UniProtKB
[32]
Resource
Comments X-ray Diffraction
Medline ID
PubMed ID 15961103
Journal J Mol Biol
Year 2005
Volume 350
Pages 489-98
Authors Arolas JL, Popowicz GM, Lorenzo J, Sommerhoff CP, Huber R, Aviles FX, Holak TA
Title The three-dimensional structures of tick carboxypeptidase inhibitor in complex with A/B carboxypeptidases reveal a novel double-headed binding mode.
Related PDB 1zli
Related UniProtKB

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.

Created Updated
2004-07-06 2009-02-26