3c3e: Difference between revisions
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< | ==Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46== | ||
<StructureSection load='3c3e' size='340' side='right'caption='[[3c3e]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3c3e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei_Go1 Methanosarcina mazei Go1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C3E 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]] 3Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FO1:1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5-B]QUINOLIN-10(2H)-YL)-D-RIBITOL'>FO1</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3c3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c3e OCA], [https://pdbe.org/3c3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c3e RCSB], [https://www.ebi.ac.uk/pdbsum/3c3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c3e ProSAT], [https://www.topsan.org/Proteins/NESGC/3c3e TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/COFD_METMA COFD_METMA] Catalyzes the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP (By similarity). | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c3/3c3e_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=3c3e ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and P(i) or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction. | |||
Molecular insights into the biosynthesis of the F420 coenzyme.,Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L J Biol Chem. 2008 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724<ref>PMID:18252724</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3c3e" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Methanosarcina mazei Go1]] | |||
[[Category: Abashidze M]] | |||
== | [[Category: Acton TB]] | ||
< | [[Category: Chen Y]] | ||
[[Category: Methanosarcina mazei | [[Category: Forouhar F]] | ||
[[Category: Abashidze | [[Category: Galinier A]] | ||
[[Category: Acton | [[Category: Grochowski LL]] | ||
[[Category: Chen | [[Category: Hussain M]] | ||
[[Category: Forouhar | [[Category: Kuzin AP]] | ||
[[Category: Galinier | [[Category: Montelione GT]] | ||
[[Category: Grochowski | [[Category: Seetharaman J]] | ||
[[Category: Hussain | [[Category: Tong L]] | ||
[[Category: Kuzin | [[Category: White RH]] | ||
[[Category: Montelione | [[Category: Xiao R]] | ||
[[Category: Xu H]] | |||
[[Category: Seetharaman | [[Category: Zhou W]] | ||
[[Category: Tong | |||
[[Category: White | |||
[[Category: Xiao | |||
[[Category: Xu | |||
[[Category: Zhou | |||
Latest revision as of 08:43, 17 October 2024
Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46
Structural highlights
FunctionCOFD_METMA Catalyzes the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP (By similarity). 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 PubMedCoenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and P(i) or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction. Molecular insights into the biosynthesis of the F420 coenzyme.,Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L J Biol Chem. 2008 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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