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[[Image:3c3e.jpg|left|200px]]


{{Structure
==Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46==
|PDB= 3c3e |SIZE=350|CAPTION= <scene name='initialview01'>3c3e</scene>, resolution 3.00&Aring;
<StructureSection load='3c3e' size='340' side='right'caption='[[3c3e]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Fo1+Binding+Site+For+Residue+A+401'>AC1</scene>, <scene name='pdbsite=AC2:Fo1+Binding+Site+For+Residue+B+401'>AC2</scene>, <scene name='pdbsite=AC3:Fo1+Binding+Site+For+Residue+C+401'>AC3</scene>, <scene name='pdbsite=AC4:Fo1+Binding+Site+For+Residue+D+401'>AC4</scene>, <scene name='pdbsite=AC5:Gdp+Binding+Site+For+Residue+A+402'>AC5</scene>, <scene name='pdbsite=AC6:Gdp+Binding+Site+For+Residue+B+402'>AC6</scene>, <scene name='pdbsite=AC7:Gdp+Binding+Site+For+Residue+C+402'>AC7</scene> and <scene name='pdbsite=AC8:Gdp+Binding+Site+For+Residue+D+402'>AC8</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=FO1:'>FO1</scene> and <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>
<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>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
|GENE= cofD, MM_1874 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192952 Methanosarcina mazei Go1])
<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.


'''Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46'''
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==Overview==
</div>
Coenzyme F420, a hydride carrier, is found in archaea and some bacteria and has crucial roles in methanogenesis, antibiotics biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-L-lactate transferase, catalyzes the last step in the biosynthesis of F420-0 (F420 without polyglutamate), by transferring the lactyl phosphate (LP) moiety of lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F420-producing organisms, and weak sequence homologs are also found in non-F420-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 Pi 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 F420 coenzyme. Large structural differences in the active site region of the non-F420-producing CofD homologs suggest that they catalyze a different biochemical reaction.
<div class="pdbe-citations 3c3e" style="background-color:#fffaf0;"></div>
 
== References ==
==About this Structure==
<references/>
3C3E is a [[Single protein]] structure of sequence from [http://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].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
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 Feb 5;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18252724 18252724]
[[Category: Methanosarcina mazei Go1]]
[[Category: Methanosarcina mazei go1]]
[[Category: Abashidze M]]
[[Category: Single protein]]
[[Category: Acton TB]]
[[Category: Abashidze, M.]]
[[Category: Chen Y]]
[[Category: Acton, T B.]]
[[Category: Forouhar F]]
[[Category: Chen, Y.]]
[[Category: Galinier A]]
[[Category: Forouhar, F.]]
[[Category: Grochowski LL]]
[[Category: Galinier, A.]]
[[Category: Hussain M]]
[[Category: Grochowski, L L.]]
[[Category: Kuzin AP]]
[[Category: Hussain, M.]]
[[Category: Montelione GT]]
[[Category: Kuzin, A P.]]
[[Category: Seetharaman J]]
[[Category: Montelione, G T.]]
[[Category: Tong L]]
[[Category: NESG, Northeast Structural Genomics Consortium.]]
[[Category: White RH]]
[[Category: Seetharaman, J.]]
[[Category: Xiao R]]
[[Category: Tong, L.]]
[[Category: Xu H]]
[[Category: White, R H.]]
[[Category: Zhou W]]
[[Category: Xiao, R.]]
[[Category: Xu, H.]]
[[Category: Zhou, W.]]
[[Category: FO1]]
[[Category: GDP]]
[[Category: alpha-beta protein]]
[[Category: magnesium]]
[[Category: nesg]]
[[Category: northeast structural genomics consortium]]
[[Category: protein structure initiative]]
[[Category: psi-2]]
[[Category: structural genomic]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:02:25 2008''

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

3c3e is a 4 chain structure with sequence from Methanosarcina mazei Go1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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

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

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[1]

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

References

  1. ↑ 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. Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem. 2008 Apr 25;283(17):11832-40. Epub 2008 Feb 5. PMID:18252724 doi:10.1074/jbc.M710352200

3c3e, resolution 3.00Å

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