PDBsum entry 1bcr

Hydrolase/hydrolase inhibitor

PDB id: 1bcr

Contents

Protein chains

254 a.a. *

152 a.a. *

Ligands

VAL-OAR

NAG-FUC-NAG

NAG-NAG

NAG

ARG

Waters ×192

* Residue conservation analysis

PDB id:

1bcr

Name:

Hydrolase/hydrolase inhibitor

Title:

Complex of the wheat serine carboxypeptidase, cpdw-ii, with the microbial peptide aldehyde inhibitor, antipain, and arginine at room temperature

Structure:

Serine carboxypeptidase ii. Chain: a. Serine carboxypeptidase ii. Chain: b. Antipain. Chain: c. Engineered: yes

Source:

Triticum aestivum. Bread wheat. Organism_taxid: 4565. Tissue: wheat germ. Synthetic: yes. Actinobacteria. Organism_taxid: 1760

Resolution:

2.50Å R-factor: 0.162

Authors:

T.L.Bullock,S.J.Remington

Key ref:

T.L.Bullock et al. (1996). Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity. J Mol Biol, 255, 714-725. PubMed id: 8636973 DOI: 10.1006/jmbi.1996.0058

Date:

03-Nov-95 Release date: 08-Mar-96

Protein chain

P08819  (CBP2_WHEAT) -  Serine carboxypeptidase 2 from Triticum aestivum

Seq: 444 a.a.

Struc: 254 a.a.

Protein chain

P08819  (CBP2_WHEAT) -  Serine carboxypeptidase 2 from Triticum aestivum

Seq: 444 a.a.

Struc: 152 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.16.6 - carboxypeptidase D.
• Reaction: Preferential release of a C-terminal arginine or lysine residue.

DOI no: 10.1006/jmbi.1996.0058

J Mol Biol 255:714-725 (1996)

PubMed id: 8636973

Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity.

T.L.Bullock, K.Breddam, S.J.Remington.

ABSTRACT

The structures of two ternary complexes of wheat serine carboxypeptidase II (CPD-WII), with a tetrapeptide aldehyde and a reaction product arginine, have been determined by X-ray crystallography at room temperature and -170 degrees. The peptide aldehydes, antipain and chymostatin, form covalent adducts with the active-site serine 146. The CPD-WII antipain arginine model has a standard crystallographic R-factor of 0.162, with good geometry at 2.5 A resolution for data collected at room temperature. The -170 degrees C model of the chymostatin arginine complex has an R-factor of 0.174, with good geometry using data to 2.1 A resolution. The structures suggest binding subsites N-terminal to the scissile bond. All four residues of chymostatin are well-localized in the putative S1 through S4 sites, while density is apparent only in S1 and S2 for antipain. In the S1 site, Val340 and 341, Phe215 and Leu216 form a hydrophobic binding surface, not a pocket, for the P1 phenylalanyl side-chain of chymostatin. The P1 arginyl of antipain also binds at this site, but the positive charge appears to be stabilized by additional solvent molecules. Thus, the hybrid nature of the S1 site accounts for the ability of CPD-WII to accept both hydrophobic and basic residues at P1. Hydrogen bonds to the peptide substrate backbone are few and are made primarily with side-chains on the enzyme. Thus, substrate recognition by CPD-WII appears to have nothing in common with that of the other families of serine proteinases. The hemiacetal linkages to the essential Ser146 are of a single stereoisomer with tetrahedral geometry, with an oxygen atom occupying the "oxyanion hole" region of the enzyme. This atom accepts three hydrogen bonds, two from the polypeptide backbone and one from the positively-charged amino group of bound arginine, and must be negatively charged. Thus, the combination of ligands forms an excellent approximation to the oxyanion intermediate formed during peptide hydrolysis. Surprisingly, the (R) stereochemistry at the hemiacetal linkage is opposite to that expected by comparison to previously determined structures of peptide aldehydes complexed with Streptomyces griseus proteinase A. This is shown to be a consequence of the approximate mirror symmetry of the arrangement of catalytic groups in the two families of serine proteases and suggests that the stereochemical course of the two enzymatic reactions differ in handedness.

Selected figure(s)

Figure 1.
Figure 1. The chemical structures of the peptide aldehydes, antipain and chymostatin from Streptomyces. Chymostatin is isolated as a mixture of three forms, A, B, and C. These have R groups of leucine (A), valine (B), or isoleucine (C) side-chains.

Figure 5.
Figure 5. (a) Stereo view of the hydrogen bonding pattern for chy- mostatin (filled bonds) from the refined -170° model. The hydrogen bonds are shown as fine lines and have the indicated lengths in Å . The adjoining residues (open bonds) of CPD-WII form one wall of the active site cavity. (b) Schematic diagram of the hydrogen bond and van der Waals' interactions of the chymo- statin/CPD-WII complex. The bold curves indicate van der Waals' contacts with side-chains of the residues indicated, while broken (b) lines indicate hydrogen bonds.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 255, 714-725) copyright 1996.

Figures were selected by an automated process.