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Overview for MACiE Entry M0005

Version history

General Information

EC Number: 3.4.16.6 (A member of the Hydrolases, Acting on peptide bonds (peptidases), Serine-type carboxypeptidases)

Enzyme Name: carboxypeptidase D

Biological Species: Triticum aestivum (Wheat)

Catalytic Chain UniprotKB Accession Codes:

  • P08819 - Serine carboxypeptidase 2 chain B

Representative PDB Code: 1whs - STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINECARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION (Resolution = 2.00 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of polypeptide n

Image of water

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Image of polypeptide n-1

polypeptide n
C00403
CHEBI:15841
water
C00001
CHEBI:15377
amino acid
C00045
CHEBI:33704
polypeptide n-1
C00403
CHEBI:15841

Overall Comment: The reference states that this mechanism was elucidated at low pH. This enzyme specifically removes basic or hydrophobic amino acid residues from the C-terminus of the peptide substrate.


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Stepwise Description of the Reaction

Step 1His397, of the Ser146-His397-Asp338 triad, deprotonates Ser146.
Step 2Ser146 attacks the carbonyl carbon of the substrate in a nucleophilic addition, resulting in the formation of a tetrahedral intermediate.
Step 3The tetrahedral intermediate collapses, cleaving the C-N bond, the nitrogen of which deprotonates His397.
Step 4His397 deprotonates water, which initiates a nucleophilic attack upon the carbonyl carbon of the acyl-enzyme substrate, forming a tetrahedral intermediate.
Step 5The tetrahedral intermediate collapses, eliminating Ser146, which deprotonates His397.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Gly 53 A Main Chain Amide
Ser 146 A Side Chain
Tyr 147 A Main Chain Amide
Asp 338 B Side Chain
His 397 B Side Chain

References

  1. T. L. Bullock et al. (1994), Biochemistry, 33, 11127-11134. Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0-A resolution.
    Medline: 7727364

Homologue information for M0005 (1whs)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0248 chloride peroxidase
1.11.1.10
1a7u 3.40.50.1820
0.62790.4430Compare
M0218 triacylglycerol lipase
3.1.1.3
1hpl 3.40.50.1820
0.75750.3856Compare
M0169 dipeptidyl-peptidase IV
3.4.14.5
1pfq 3.40.50.1820
10.6606Compare
M0217 hydroxynitrilase
4.1.2.37
1sc9 3.40.50.1820
0.27270.3856Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.1820


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
carboxypeptidase activity (molecular function)
serine-type carboxypeptidase activity (molecular function)
proteolysis (biological process)
peptidase activity (molecular function)
hydrolase activity (molecular function)
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