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| - | [[Image:1xgo.jpg|left|200px]]<br /><applet load="1xgo" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1xgo, resolution 3.5Å" /> | |
| - | '''METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS'''<br /> | |
| | | | |
| - | ==Overview== | + | ==METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS== |
| - | 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. | + | <StructureSection load='1xgo' size='340' side='right'caption='[[1xgo]], [[Resolution|resolution]] 3.50Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1xgo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XGO FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5Å</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xgo OCA], [https://pdbe.org/1xgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xgo RCSB], [https://www.ebi.ac.uk/pdbsum/1xgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xgo ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/MAP2_PYRFU MAP2_PYRFU] Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val).[HAMAP-Rule:MF_01975]<ref>PMID:9399590</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xg/1xgo_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xgo ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | 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. |
| | | | |
| - | ==About this Structure==
| + | Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.,Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I J Mol Biol. 1998 Nov 20;284(1):101-24. PMID:9811545<ref>PMID:9811545</ref> |
| - | 1XGO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Active as [http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] Known structural/functional Site: <scene name='pdbsite=AC:Side Chains Of Five Amino Acid Residues ASP 82, ASP 93, ...'>AC</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XGO OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus., Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I, J Mol Biol. 1998 Nov 20;284(1):101-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9811545 9811545]
| + | </div> |
| - | [[Category: Methionyl aminopeptidase]]
| + | <div class="pdbe-citations 1xgo" style="background-color:#fffaf0;"></div> |
| - | [[Category: Pyrococcus furiosus]]
| + | |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Tahirov, T.H.]]
| + | |
| - | [[Category: Tsukihara, T.]]
| + | |
| - | [[Category: aminopeptidase]]
| + | |
| - | [[Category: hyperthermophile]]
| + | |
| | | | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 18:39:24 2007''
| + | ==See Also== |
| | + | *[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Pyrococcus furiosus]] |
| | + | [[Category: Tahirov TH]] |
| | + | [[Category: Tsukihara T]] |
| Structural highlights
Function
MAP2_PYRFU Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val).[HAMAP-Rule:MF_01975][1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.,Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I J Mol Biol. 1998 Nov 20;284(1):101-24. PMID:9811545[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tsunasawa S, Izu Y, Miyagi M, Kato I. Methionine aminopeptidase from the hyperthermophilic Archaeon Pyrococcus furiosus: molecular cloning and overexpression in Escherichia coli of the gene, and characteristics of the enzyme. J Biochem. 1997 Oct;122(4):843-50. PMID:9399590 doi:10.1093/oxfordjournals.jbchem.a021831
- ↑ Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. J Mol Biol. 1998 Nov 20;284(1):101-24. PMID:9811545 doi:10.1006/jmbi.1998.2146
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