3o61: Difference between revisions
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==Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++== | |||
<StructureSection load='3o61' size='340' side='right'caption='[[3o61]], [[Resolution|resolution]] 2.45Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3o61]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O61 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]] 2.45Å</td></tr> | |||
<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=GDD:GUANOSINE-5-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=3o61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o61 OCA], [https://pdbe.org/3o61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o61 RCSB], [https://www.ebi.ac.uk/pdbsum/3o61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o61 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NUDK_ECOLI NUDK_ECOLI] Catalyzes the hydrolysis of GDP-mannose. Can also use other substrates, catalyzing the hydrolysis of the pyrophosphate bond, releasing a nucleoside monophosphate and a phosphorylated moiety, depending on the substrate.<ref>PMID:16766526</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX(5) EX(7) REUXEEXGU (where U is I, L, or V), is a well-studied family in which relations have been established between primary sequence and substrate specificity for many members. For example, enzymes that hydrolyze the diphosphate linkage of ADP-ribose are characterized by having a proline 15 amino acids C-terminal of the Nudix signature sequence. GDPMK is a Nudix enzyme that conserves this characteristic proline but uses GDP-mannose as the preferred substrate. By investigating the structure of the GDPMK alone, bound to magnesium, and bound to substrate, the structural basis for this divergent substrate specificity and a new rule was identified by which ADP-ribose pyrophosphatases can be distinguished from purine-DP-mannose pyrophosphatases from primary sequence alone. Kinetic and mutagenesis studies showed that GDPMK hydrolysis does not rely on a single glutamate as the catalytic base. Instead, catalysis is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. GDPMK was thought to play a role in biofilm formation because of its upregulation in response to RcsC signaling; however, GDPMK knockout strains show no defect in their capacity of forming biofilms. Proteins 2011; (c) 2011 Wiley-Liss, Inc. | |||
Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.,Boto AN, Xu W, Jakoncic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, Amzel LM Proteins. 2011 Aug;79(8):2455-66. doi: 10.1002/prot.23069. Epub 2011 Jun, 2. PMID:21638333<ref>PMID:21638333</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3o61" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli K-12]] | |||
[[Category: Large Structures]] | |||
[[Category: Amzel LM]] | |||
[[Category: Boto AN]] | |||
[[Category: Gabelli SB]] | |||
Latest revision as of 12:29, 6 September 2023
Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++
Structural highlights
FunctionNUDK_ECOLI Catalyzes the hydrolysis of GDP-mannose. Can also use other substrates, catalyzing the hydrolysis of the pyrophosphate bond, releasing a nucleoside monophosphate and a phosphorylated moiety, depending on the substrate.[1] Publication Abstract from PubMedThe Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX(5) EX(7) REUXEEXGU (where U is I, L, or V), is a well-studied family in which relations have been established between primary sequence and substrate specificity for many members. For example, enzymes that hydrolyze the diphosphate linkage of ADP-ribose are characterized by having a proline 15 amino acids C-terminal of the Nudix signature sequence. GDPMK is a Nudix enzyme that conserves this characteristic proline but uses GDP-mannose as the preferred substrate. By investigating the structure of the GDPMK alone, bound to magnesium, and bound to substrate, the structural basis for this divergent substrate specificity and a new rule was identified by which ADP-ribose pyrophosphatases can be distinguished from purine-DP-mannose pyrophosphatases from primary sequence alone. Kinetic and mutagenesis studies showed that GDPMK hydrolysis does not rely on a single glutamate as the catalytic base. Instead, catalysis is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. GDPMK was thought to play a role in biofilm formation because of its upregulation in response to RcsC signaling; however, GDPMK knockout strains show no defect in their capacity of forming biofilms. Proteins 2011; (c) 2011 Wiley-Liss, Inc. Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.,Boto AN, Xu W, Jakoncic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, Amzel LM Proteins. 2011 Aug;79(8):2455-66. doi: 10.1002/prot.23069. Epub 2011 Jun, 2. PMID:21638333[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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