1rya: Difference between revisions

Revision as of 06:36, 25 December 2014

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

Structural highlights

1rya is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CL, GDP, MG, TRS
Gene:	NUDD, WCAH, GMM, B2051 (Escherichia coli)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[NUDD_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.^[1] ^[2]

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

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.

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:15274914^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Frick DN, Townsend BD, Bessman MJ. A novel GDP-mannose mannosyl hydrolase shares homology with the MutT family of enzymes. J Biol Chem. 1995 Oct 13;270(41):24086-91. PMID:7592609
↑ Legler PM, Massiah MA, Bessman MJ, Mildvan AS. GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at carbon, unlike all other Nudix hydrolases. Biochemistry. 2000 Jul 25;39(29):8603-8. PMID:10913267
↑ Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM. Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure. 2004 Jun;12(6):927-35. PMID:15274914 doi:10.1016/j.str.2004.03.028

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Frick DN, Townsend BD, Bessman MJ. A novel GDP-mannose mannosyl hydrolase shares homology with the MutT family of enzymes. J Biol Chem. 1995 Oct 13;270(41):24086-91. PMID:7592609

[2] Legler PM, Massiah MA, Bessman MJ, Mildvan AS. GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at carbon, unlike all other Nudix hydrolases. Biochemistry. 2000 Jul 25;39(29):8603-8. PMID:10913267

[3] Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM. Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure. 2004 Jun;12(6):927-35. PMID:15274914 doi:10.1016/j.str.2004.03.028

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1rya]] is a 2 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RYA FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDD, WCAH, GMM, B2051 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDD, WCAH, GMM, B2051 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rya OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rya RCSB], [http://www.ebi.ac.uk/pdbsum/1rya PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rya OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rya RCSB], [http://www.ebi.ac.uk/pdbsum/1rya PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/NUDD_ECOLI NUDD_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:7592609</ref> <ref>PMID:10913267</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 32: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Amzel, L M.]]
+[[Category: Amzel, L M]]
-[[Category: Bianchet, M A.]]
+[[Category: Bianchet, M A]]
-[[Category: Gabelli, S B.]]
+[[Category: Gabelli, S B]]
-[[Category: Legler, P M.]]
+[[Category: Legler, P M]]
-[[Category: Mildvan, A S.]]
+[[Category: Mildvan, A S]]
 [[Category: Gdp-glucose]]
 [[Category: Gdp-mannose]]

1rya: Difference between revisions

Revision as of 06:36, 25 December 2014

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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