|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium== | | ==Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium== |
| - | <StructureSection load='4ryu' size='340' side='right' caption='[[4ryu]], [[Resolution|resolution]] 2.04Å' scene=''> | + | <StructureSection load='4ryu' size='340' side='right'caption='[[4ryu]], [[Resolution|resolution]] 2.04Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ryu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_enteritidis_str._ec20130345 Salmonella enterica subsp. enterica serovar enteritidis str. ec20130345]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RYU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ryu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._EC20130345 Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130345]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RYU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v4n|2v4n]], [[2v4o|2v4o]], [[4g9o|4g9o]], [[4gad|4gad]], [[4ryt|4ryt]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AV66_15865, surE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1412588 Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130345])</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=4ryu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryu OCA], [https://pdbe.org/4ryu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ryu RCSB], [https://www.ebi.ac.uk/pdbsum/4ryu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryu ProSAT]</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=4ryu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryu OCA], [http://pdbe.org/4ryu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ryu RCSB], [http://www.ebi.ac.uk/pdbsum/4ryu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY]] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060] | + | [https://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Salmonella enterica subsp. enterica serovar enteritidis str. ec20130345]] | + | [[Category: Large Structures]] |
| - | [[Category: Mathiharan, Y K]] | + | [[Category: Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130345]] |
| - | [[Category: Murthy, M R.N]] | + | [[Category: Mathiharan YK]] |
| - | [[Category: Domain swapping]]
| + | [[Category: Murthy MRN]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Phosphatase]]
| + | |
| - | [[Category: Rossmann fold like]]
| + | |
| - | [[Category: Stationary phase survival protein]]
| + | |
| Structural highlights
Function
SURE_SALTY Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]
Publication Abstract from PubMed
The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees . New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.
Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.,Mathiharan YK, Savithri HS, Murthy MR Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1812-23. doi:, 10.1107/S1399004715011992. Epub 2015 Aug 25. PMID:26327371[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mathiharan YK, Savithri HS, Murthy MR. Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1812-23. doi:, 10.1107/S1399004715011992. Epub 2015 Aug 25. PMID:26327371 doi:http://dx.doi.org/10.1107/S1399004715011992
|
