1rya: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1rya.jpg|left|200px]]


{{Structure
==Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG==
|PDB= 1rya |SIZE=350|CAPTION= <scene name='initialview01'>1rya</scene>, resolution 1.30&Aring;
<StructureSection load='1rya' size='340' side='right'caption='[[1rya]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene> and <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
<table><tr><td colspan='2'>[[1rya]] is a 2 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=1RYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYA FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
|GENE= NUDD, WCAH, GMM, B2051 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1rya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rya OCA], [https://pdbe.org/1rya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rya RCSB], [https://www.ebi.ac.uk/pdbsum/1rya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rya ProSAT]</span></td></tr>
 
</table>
'''Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG'''
== Function ==
 
[https://www.uniprot.org/uniprot/GMM_ECOLI GMM_ECOLI] Hydrolyzes both GDP-mannose and GDP-glucose. Could participate in the regulation of cell wall biosynthesis by influencing the concentration of GDP-mannose or GDP-glucose in the cell. Might also be involved in the biosynthesis of the slime polysaccharide colanic acid.<ref>PMID:10913267</ref> <ref>PMID:7592609</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 A X-ray structure of the GDPMH-Mg(2+)-GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction. Several residues and the divalent cation strongly promote the departure of the GDP leaving group, supporting a dissociative mechanism. Comparison of the GDPMH structure with that of a typical Nudix hydrolase suggests how sequence changes result in the switch of catalytic activity from P-O bond cleavage to C-O bond cleavage. Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ry/1rya_consurf.spt"</scriptWhenChecked>
1RYA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYA OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus., Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM, Structure. 2004 Jun;12(6):927-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15274914 15274914]
</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=1rya ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Amzel, L M.]]
[[Category: Amzel LM]]
[[Category: Bianchet, M A.]]
[[Category: Bianchet MA]]
[[Category: Gabelli, S B.]]
[[Category: Gabelli SB]]
[[Category: Legler, P M.]]
[[Category: Legler PM]]
[[Category: Mildvan, A S.]]
[[Category: Mildvan AS]]
[[Category: CL]]
[[Category: GDP]]
[[Category: MG]]
[[Category: TRS]]
[[Category: gdp-glucose]]
[[Category: gdp-mannose]]
[[Category: mannose]]
[[Category: nudix]]
[[Category: nudix mg-complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:57:52 2008''
Retrieved from "https://proteopedia.org/1rya"