PDBsum entry 1xgo

Aminopeptidase

PDB id: 1xgo

Contents

Protein chain

295 a.a. *

* Residue conservation analysis

PDB id:

1xgo

Name:

Aminopeptidase

Title:

Methionine aminopeptidase from hyperthermophile pyrococcus furiosus

Structure:

Methionine aminopeptidase. Chain: a. Other_details: two cobalt ions in active site removed by the reduction of ph to 2.6

Source:

Pyrococcus furiosus. Organism_taxid: 2261

Resolution:

3.50Å R-factor: 0.182 R-free: 0.274

Authors:

T.H.Tahirov,T.Tsukihara

Key ref:

T.H.Tahirov et al. (1998). Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. J Mol Biol, 284, 101-124. PubMed id: 9811545 DOI: 10.1006/jmbi.1998.2146

Date:

18-Nov-97 Release date: 25-Feb-98

Protein chain

P56218  (MAP2_PYRFU) -  Methionine aminopeptidase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 295 a.a.

Struc: 295 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.11.18 - methionyl aminopeptidase.
• Reaction: Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
• Cofactor: Cobalt cation

DOI no: 10.1006/jmbi.1998.2146

J Mol Biol 284:101-124 (1998)

PubMed id: 9811545

Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.

T.H.Tahirov, H.Oki, T.Tsukihara, K.Ogasahara, K.Yutani, K.Ogata, Y.Izu, S.Tsunasawa, I.Kato.

ABSTRACT

The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100 degreesC was determined by the multiple isomorphous replacement method and refined in three different crystal forms, one monoclinic and two hexagonal, at resolutions of 2.8, 2.9, and 3.5 A. The resolution of the monoclinic crystal form was extended to 1.75 A by water-mediated transformation to a low-humidity form, and the obtained diffraction data used for high-resolution structure refinement. This is the first description of a eukaryotic type methionine aminopeptidase structure. The PfMAP molecule is composed of two domains, a catalytic domain and an insertion domain, connected via two antiparallel beta-strands. The catalytic domain, which possesses an internal 2-fold symmetry and contains two cobalt ions in the active site, resembles the structure of a prokaryotic type MAP from Escherichia coli (EcMAP), while the structure of the insertion domain containing three helices has a novel fold and accounts for a major difference between the eukaryotic and prokaryotic types of methionine aminopeptidase. Analysis of the PfMAP structure in comparison with EcMAP and other mesophile proteins reveals several factors which may contribute to the hyperthermostability of PfMAP: (1) a significantly high number of hydrogen bonds and ion-pairs between side-chains of oppositely charged residues involved in the stabilization of helices; (2) an increased number of hydrogen bonds between the positively charged side-chain and neutral oxygen; (3) a larger number of buried water molecules involved in crosslinking the backbone atoms of sequentially separate segments; (4) stabilization of two antiparallel beta-strands connecting the two domains of the molecule by proline residues; (5) shortening of N and C-terminal tails and stabilization of the loop c3E by deletion of three residues.

Selected figure(s)

Figure 2.
Figure 2. The arrangement of proline residues Pro201, Pro202, and Pro266 in strands c2 and c3. Hydrogen bonds are shown by broken lines.

Figure 6.
Figure 6. Ion-pairs (a) in PfMAP, molecule lhf-A1, and (b) EcMAP. The a-carbon traces are shown by thin continuous lines, and the side-chains of charged residues forming the ion-pairs are shown by continuous bold lines. The interactions between the oppositely charged atoms with distance cutoff of 4 Å (broken lines).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 101-124) copyright 1998.

Figures were selected by an automated process.