PDBsum entry 1m4l

Hydrolase

PDB id: 1m4l

Contents

Protein chain

307 a.a. *

Metals

_ZN

Waters ×375

* Residue conservation analysis

PDB id:

1m4l

Name:

Hydrolase

Title:

Structure of native carboxypeptidase a at 1.25 resolution

Structure:

Carboxypeptidase a. Chain: a. Ec: 3.4.17.1

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Resolution:

1.25Å R-factor: 0.104 R-free: 0.145

Authors:

A.Kilshtain-Vardi,M.Glick,H.M.Greenblatt,A.Goldblum,G.Shoham

Key ref:

A.Kilshtain-Vardi et al. (2003). Refined structure of bovine carboxypeptidase A at 1.25 A resolution. Acta Crystallogr D Biol Crystallogr, 59, 323-333. PubMed id: 12554943 DOI: 10.1107/S0907444902015706

Date:

03-Jul-02 Release date: 10-Jan-03

Protein chain

P00730  (CBPA1_BOVIN) -  Carboxypeptidase A1 from Bos taurus

Seq: 419 a.a.

Struc: 307 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.17.1 - carboxypeptidase A.
• Reaction: Peptidyl-L-amino acid + H₂O = peptide + L-amino acid
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1107/S0907444902015706

Acta Crystallogr D Biol Crystallogr 59:323-333 (2003)

PubMed id: 12554943

Refined structure of bovine carboxypeptidase A at 1.25 A resolution.

A.Kilshtain-Vardi, M.Glick, H.M.Greenblatt, A.Goldblum, G.Shoham.

ABSTRACT

The crystal structure of the bovine zinc metalloproteinase carboxypeptidase A (CPA) has been refined to 1.25 A resolution based on room-temperature X-ray synchrotron data. The significantly improved structure of CPA at this resolution (anisotropic temperature factors, R factor = 10.4%, R(free) = 14.5%) allowed the modelling of conformational disorders of side chains, improved the description of the protein solvent network (375 water molecules) and provided a more accurate picture of the interactions between the active-site zinc and its ligands. The calculation of standard uncertainties in individual atom positions of the refined model of CPA allowed the deduction of the protonation state of some key residues in the active site and confirmed that Glu72 and Glu270 are negatively charged in the resting state of the enzyme at pH 7.5. These results were further validated by theoretical calculations that showed significant reduction of the pK(a) of these side chains relative to solution values. The distance between the zinc-bound solvent molecule and the metal ion is strongly suggestive of a neutral water molecule and not a hydroxide ion in the resting state of the enzyme. These findings could support both the general acid/general base mechanism, as well as the anhydride mechanism suggested for CPA.

Selected figure(s)

Figure 1.
Figure 1 Electron-density `omit' map around the active site of native CPA at 1.25 Å resolution. Electron-density contour levels are at +4.5 (cyan). Superimposed on the density is the final 1.25 Å model of CPA (ball-and-stick representation, common atom colour codes), featuring the zinc and its ligands, as well as the catalytic residues Arg127 and Glu270.

Figure 5.
Figure 5 A stereoview of the active site of native CPA (stick model) following the proton-addition algorithm. Atoms are coloured according to conventional codes (C atoms, yellow; N atoms, blue; O atoms, red; H atoms, white; Zn atoms, purple). Zinc-ligand interactions are indicated (dashed lines) and their distances are displayed (Å). The zinc-bound water is indicated by `W'.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 323-333) copyright 2003.

Figures were selected by an automated process.