1mat: Difference between revisions

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New page: left|200px<br /><applet load="1mat" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mat, resolution 2.4Å" /> '''STRUCTURE OF THE COBA...
 
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[[Image:1mat.jpg|left|200px]]<br /><applet load="1mat" size="450" color="white" frame="true" align="right" spinBox="true"
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'''STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME'''<br />


==Overview==
==STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME==
The X-ray structure of Escherichia coli methionine aminopeptidase (MAP), has been determined to 2.4-A resolution and refined to a crystallographic, R-factor of 18.2%. The fold is novel and displays internal pseudo-2-fold, symmetry which structurally relates the first and second halves of the, polypeptide chain. The topology consists of a central antiparallel, beta-sheet covered on one side by two pairs of alpha-helices and by a, C-terminal loop. The other face of the beta-sheet, together with some, irregular loops, forms the active site, which contains two cobalt ions 2.9, A apart. These metal ions are liganded by the side chains of Asp 97, Asp, 108, Glu 204, Glu 235, and His 171 with approximate octahedral, coordination. In terms of both the novel backbone fold and the, constitution of the active site, MAP appears to represent a new class of, proteolytic enzyme.
<StructureSection load='1mat' size='340' side='right'caption='[[1mat]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1mat]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MAT 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></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=1mat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mat OCA], [https://pdbe.org/1mat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mat RCSB], [https://www.ebi.ac.uk/pdbsum/1mat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mat ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MAP1_ECOLI MAP1_ECOLI] 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). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed.[HAMAP-Rule:MF_01974]<ref>PMID:20521764</ref> <ref>PMID:3027045</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/ma/1mat_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=1mat ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1MAT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CO as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MAT OCA].
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 
== References ==
==Reference==
<references/>
Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme., Roderick SL, Matthews BW, Biochemistry. 1993 Apr 20;32(15):3907-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8471602 8471602]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Methionyl aminopeptidase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Matthews BW]]
[[Category: Matthews, B.W.]]
[[Category: Roderick SL]]
[[Category: Roderick, S.L.]]
[[Category: CO]]
[[Category: hydrolase(alpha-aminoacylpeptide)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:17:02 2007''

Latest revision as of 10:42, 14 February 2024

STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYMESTRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME

Structural highlights

1mat is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MAP1_ECOLI 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). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed.[HAMAP-Rule:MF_01974][1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Xiao Q, Zhang F, Nacev BA, Liu JO, Pei D. Protein N-terminal processing: substrate specificity of Escherichia coli and human methionine aminopeptidases. Biochemistry. 2010 Jul 6;49(26):5588-99. doi: 10.1021/bi1005464. PMID:20521764 doi:http://dx.doi.org/10.1021/bi1005464
  2. ↑ Ben-Bassat A, Bauer K, Chang SY, Myambo K, Boosman A, Chang S. Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure. J Bacteriol. 1987 Feb;169(2):751-7. PMID:3027045

1mat, resolution 2.40Å

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