PDBsum entry 1bpn

Hydrolase(alpha-aminoacylpeptide)

PDB id: 1bpn

Contents

Protein chain

481 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1bpn

Name:

Hydrolase(alpha-aminoacylpeptide)

Title:

Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography

Structure:

Leucine aminopeptidase. Chain: a. Engineered: yes

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Tissue: lens

Biol. unit:

Hexamer (from PQS)

Resolution:

2.90Å R-factor: 0.188

Authors:

H.Kim,W.N.Lipscomb

Key ref:

H.Kim and W.N.Lipscomb (1993). Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography. Proc Natl Acad Sci U S A, 90, 5006-5010. PubMed id: 8506345 DOI: 10.1073/pnas.90.11.5006

Date:

02-Mar-93 Release date: 15-Jul-93

Protein chain

P00727  (AMPL_BOVIN) -  Cytosol aminopeptidase from Bos taurus

Seq: 519 a.a.

Struc: 481 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.4.11.1 - leucyl aminopeptidase.
• Reaction: Release of an N-terminal amino acid, Xaa-|-Xbb-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Xbb may be Pro.
• Cofactor: Zn(2+)
• Enzyme class 2: E.C.3.4.11.5 - prolyl aminopeptidase.
• Reaction: Release of a N-terminal proline from a peptide.
• Cofactor: Mn(2+)
• Enzyme class 3: E.C.3.4.13.23 - cysteinylglycine-S-conjugate dipeptidase.
• Reaction: an S-substituted L-cysteinylglycine + H2O = an S-substituted L-cysteine + glycine

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1073/pnas.90.11.5006

Proc Natl Acad Sci U S A 90:5006-5010 (1993)

PubMed id: 8506345

Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography.

H.Kim, W.N.Lipscomb.

ABSTRACT

The tightly binding and readily exchanging metal binding sites in the active site of bovine lens leucine aminopeptidase (blLAP; EC 3.4.11.1) have been differentiated and identified by x-ray crystallography. In native blLAP,Zn2+ occupies both binding sites. In solution, site 1 readily exchanges Zn2+ for other divalent cations, including Mg2+. The Zn2+ in site 2 is unavailable for metal exchange under conditions which allow exchange at site 1. The Zn2+/Mg2+ metal hybrid of blLAP (Mg-blLAP) was prepared in solution and crystallized. X-ray diffraction data to 2.9-A resolution were collected at -150 degrees C from single crystals of Mg-blLAP and native blLAP. Comparisons of omit maps calculated from the Mg-blLAP data with analogous maps calculated from the native blLAP data show electron density in one of the metal binding sites in Mg-blLAP which is much weaker than the electron density in the other binding site. Since there are fewer electrons associated with Mg2+ than with Zn2+, the difference in electron density between the two metal binding sites is consistent with occupancy of the weaker electron density site by Mg2+ and identifies this metal binding site as site 1, defined as the readily exchanging site. The present identification of the metal binding sites reverses the previous presumptive assignment of the metal binding sites which was based on the structure of native blLAP [Burley, S. K., David, P. R., Sweet, R. M., Taylor, A. & Lipscomb, W. N. (1992) J. Mol. Biol. 224, 113-140]. According to the residue-numbering convention of native blLAP, the new assignment of the metal binding sites identifies the readily exchanging site 1 with Zn-488, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-332, and Glu-334 and the main-chain carbonyl oxygen of Asp-332. The more tightly binding site 2 is identified with Zn-489, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-273, and Glu-334 and the side-chain amine nitrogen of Lys-250.