1n1d: Difference between revisions

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<StructureSection load='1n1d' size='340' side='right'caption='[[1n1d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1n1d' size='340' side='right'caption='[[1n1d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1n1d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1D FirstGlance]. <br>
<table><tr><td colspan='2'>[[1n1d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2G:[CYTIDINE-5-PHOSPHATE]+GLYCERYLPHOSPHORIC+ACID+ESTER'>C2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1coz|1coz]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2G:[CYTIDINE-5-PHOSPHATE]+GLYCERYLPHOSPHORIC+ACID+ESTER'>C2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycerol-3-phosphate_cytidylyltransferase Glycerol-3-phosphate cytidylyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.39 2.7.7.39] </span></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=1n1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1d OCA], [https://pdbe.org/1n1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1d RCSB], [https://www.ebi.ac.uk/pdbsum/1n1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1d ProSAT]</span></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=1n1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1d OCA], [https://pdbe.org/1n1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1d RCSB], [https://www.ebi.ac.uk/pdbsum/1n1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1d ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/TAGD_BACSU TAGD_BACSU]] Provides activated glycerol phosphate for teichoic acid synthesis, via incorporation into both the linkage unit and the teichoic acid polymer by TagB and TagF.  
[https://www.uniprot.org/uniprot/TAGD_BACSU TAGD_BACSU] Provides activated glycerol phosphate for teichoic acid synthesis, via incorporation into both the linkage unit and the teichoic acid polymer by TagB and TagF.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1n1d ConSurf].
</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=1n1d ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bacterial enzyme, glycerol-3-phosphate cytidylyltransferase (GCT), is a model for mammalian cytidylyltransferases and is a member of a large superfamily of nucleotidyltransferases. Dimeric GCT from Bacillus subtilis displays unusual negative cooperativity in substrate binding and appears to form products only when both active sites are occupied by substrates. Here we describe a complex of GCT with the product, CDP-glycerol, in a crystal structure in which bound sulfate serves as a partial mimic of the second product, pyrophosphate. Binding of sulfate to form a pseudo-ternary complex is observed in three of the four chains constituting the asymmetric unit and is accompanied by a backbone rearrangement at Asp11 and ordering of the C-terminal helix. Comparison with the CTP complex of GCT, determined previously, reveals that in the product complex the active site closes around the glycerol phosphate moiety with a concerted motion of the segment 37-47 that includes helix B. This rearrangement allows lysines 44 and 46 to interact with the glycerol and cytosine phosphates of CDP-glycerol. Binding of CDP-glycerol also induces smaller movements of residues 92-100. Roles of lysines 44 and 46 in catalysis have been confirmed by mutagenesis of these residues to alanine, which decreases Vmax(app) and has profound effects on the Km(app) for glycerol-3-phosphate.
Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis.,Pattridge KA, Weber CH, Friesen JA, Sanker S, Kent C, Ludwig ML J Biol Chem. 2003 Dec 19;278(51):51863-71. Epub 2003 Sep 23. PMID:14506262<ref>PMID:14506262</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n1d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Glycerol-3-phosphate cytidylyltransferase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Friesen, J A]]
[[Category: Friesen JA]]
[[Category: Kent, C]]
[[Category: Kent C]]
[[Category: Ludwig, M L]]
[[Category: Ludwig ML]]
[[Category: Pattridge, K A]]
[[Category: Pattridge KA]]
[[Category: Sankar, S]]
[[Category: Sankar S]]
[[Category: Weber, C H]]
[[Category: Weber CH]]
[[Category: Alpha/beta fold]]
[[Category: Cdp-glycerol]]
[[Category: Cytidylyltransferase]]
[[Category: Negative cooperativity]]
[[Category: Nucleotidyltransferase]]
[[Category: Transferase]]

Latest revision as of 10:51, 14 February 2024

Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerolGlycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol

Structural highlights

1n1d is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TAGD_BACSU Provides activated glycerol phosphate for teichoic acid synthesis, via incorporation into both the linkage unit and the teichoic acid polymer by TagB and TagF.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1n1d, resolution 2.00Å

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OCA
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