5gga

From Proteopedia

(Difference between revisions)

Revision as of 06:41, 13 May 2020

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate

Structural highlights

5gga is a 1 chain structure with sequence from Mycs2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	5gg5, 5gg6, 5gg7, 5gg8, 5gg9, 5ggb, 5ggc, 5ggd
Gene:	MSMEG_2390 (MYCS2)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate. The role of domain 2 appears to be limited to speeding up the reaction. Crystal structures of the apoenzyme and those of ligand-bound enzyme prepared in the presence of 8-oxo-GTP or 8-oxo-dGTP and different concentrations of magnesium were determined. In all of the structures except one, the molecules arrange themselves in a head-to-tail fashion in which domain 1 is brought into contact with domain 2 (trans domain 2) of a neighbouring molecule. The binding site for NTP (site A) is almost exclusively made up of residues from domain 1, while those for NDP (site B) and NMP (site C) are at the interface between domain 1 and trans domain 2 in an unusual instance of intermolecular interactions leading to binding sites. Protein-ligand interactions at site A lead to a proposal for the mechanism of hydrolysis of NTP to NDP and phosphate. A small modification in site A in the crystal which does not exhibit the head-to-tail arrangement appears to facilitate the production of NMP and pyrophosphate from NTP. The two arrangements could be in dynamic equilibrium in the cellular milieu.

Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association.,Arif SM, Patil AG, Varshney U, Vijayan M Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):349-364. doi:, 10.1107/S2059798317002534. Epub 2017 Mar 31. PMID:28375146^[1]

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

References

↑ Arif SM, Patil AG, Varshney U, Vijayan M. Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association. Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):349-364. doi:, 10.1107/S2059798317002534. Epub 2017 Mar 31. PMID:28375146 doi:http://dx.doi.org/10.1107/S2059798317002534

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5gga"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate==
-<StructureSection load='5gga' size='340' side='right' caption='[[5gga]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='5gga' size='340' side='right'caption='[[5gga]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GGA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GGA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gg5|5gg5]], [[5gg6|5gg6]], [[5gg7|5gg7]], [[5gg8|5gg8]], [[5gg9|5gg9]], [[5ggb|5ggb]], [[5ggc|5ggc]], [[5ggd|5ggd]]</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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [http://pdbe.org/5gga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [http://www.ebi.ac.uk/pdbsum/5gga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MSMEG_2390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [http://pdbe.org/5gga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [http://www.ebi.ac.uk/pdbsum/5gga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 17: / Line 18: @@
 </div>
 <div class="pdbe-citations 5gga" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycs2]]
 [[Category: Arif, S M]]
 [[Category: Patil, A G]]

5gga

From Proteopedia

Revision as of 06:41, 13 May 2020

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox