Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus

Tahir H. Tahirov, Hideyuki Oki, Tomitake Tsukihara, Kyoko Ogasahara, Katsuhide Yutani, Kazuhiro Ogata, Yukiko Izu, Susumu Tsunasawa, Ikunoshin Kato

Research output: Contribution to journalArticle

125 Citations (Scopus)

Abstract

The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100°C 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 Å. The resolution of the monoclinic crystal form was extended to 1.75 Å 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 β-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 β-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.

Original languageEnglish (US)
Pages (from-to)101-124
Number of pages24
JournalJournal of Molecular Biology
Volume284
Issue number1
DOIs
StatePublished - Nov 20 1998

Fingerprint

Pyrococcus furiosus
Aminopeptidases
Methionine
Catalytic Domain
Pair Bond
Water
Humidity
Cobalt
Proline
Protons
Hydrogen
Ions
Oxygen
Escherichia coli
Temperature
Growth
Proteins

Keywords

  • Binuclear reaction center
  • Cobalt-dependent enzyme
  • Hyperthermophile
  • Methionine aminopeptidase
  • Water-mediated crystal transformation

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. / Tahirov, Tahir H.; Oki, Hideyuki; Tsukihara, Tomitake; Ogasahara, Kyoko; Yutani, Katsuhide; Ogata, Kazuhiro; Izu, Yukiko; Tsunasawa, Susumu; Kato, Ikunoshin.

In: Journal of Molecular Biology, Vol. 284, No. 1, 20.11.1998, p. 101-124.

Research output: Contribution to journalArticle

Tahirov, TH, Oki, H, Tsukihara, T, Ogasahara, K, Yutani, K, Ogata, K, Izu, Y, Tsunasawa, S & Kato, I 1998, 'Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus', Journal of Molecular Biology, vol. 284, no. 1, pp. 101-124. https://doi.org/10.1006/jmbi.1998.2146
Tahirov, Tahir H. ; Oki, Hideyuki ; Tsukihara, Tomitake ; Ogasahara, Kyoko ; Yutani, Katsuhide ; Ogata, Kazuhiro ; Izu, Yukiko ; Tsunasawa, Susumu ; Kato, Ikunoshin. / Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. In: Journal of Molecular Biology. 1998 ; Vol. 284, No. 1. pp. 101-124.
@article{87adc861b2c5480bbfd162cf449a380b,
title = "Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus",
abstract = "The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100°C 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 {\AA}. The resolution of the monoclinic crystal form was extended to 1.75 {\AA} 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 β-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 β-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.",
keywords = "Binuclear reaction center, Cobalt-dependent enzyme, Hyperthermophile, Methionine aminopeptidase, Water-mediated crystal transformation",
author = "Tahirov, {Tahir H.} and Hideyuki Oki and Tomitake Tsukihara and Kyoko Ogasahara and Katsuhide Yutani and Kazuhiro Ogata and Yukiko Izu and Susumu Tsunasawa and Ikunoshin Kato",
year = "1998",
month = "11",
day = "20",
doi = "10.1006/jmbi.1998.2146",
language = "English (US)",
volume = "284",
pages = "101--124",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus

AU - Tahirov, Tahir H.

AU - Oki, Hideyuki

AU - Tsukihara, Tomitake

AU - Ogasahara, Kyoko

AU - Yutani, Katsuhide

AU - Ogata, Kazuhiro

AU - Izu, Yukiko

AU - Tsunasawa, Susumu

AU - Kato, Ikunoshin

PY - 1998/11/20

Y1 - 1998/11/20

N2 - The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100°C 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 Å. The resolution of the monoclinic crystal form was extended to 1.75 Å 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 β-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 β-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.

AB - The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100°C 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 Å. The resolution of the monoclinic crystal form was extended to 1.75 Å 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 β-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 β-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.

KW - Binuclear reaction center

KW - Cobalt-dependent enzyme

KW - Hyperthermophile

KW - Methionine aminopeptidase

KW - Water-mediated crystal transformation

UR - http://www.scopus.com/inward/record.url?scp=0032553557&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032553557&partnerID=8YFLogxK

U2 - 10.1006/jmbi.1998.2146

DO - 10.1006/jmbi.1998.2146

M3 - Article

C2 - 9811545

AN - SCOPUS:0032553557

VL - 284

SP - 101

EP - 124

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 1

ER -