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| | ==Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii== | | ==Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii== |
| - | <StructureSection load='3rsb' size='340' side='right' caption='[[3rsb]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='3rsb' size='340' side='right'caption='[[3rsb]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rsb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RSB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rsb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RSB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cobY, MJ1117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3rsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rsb OCA], [https://pdbe.org/3rsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rsb RCSB], [https://www.ebi.ac.uk/pdbsum/3rsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rsb ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylcobinamide-phosphate_guanylyltransferase Adenosylcobinamide-phosphate guanylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.62 2.7.7.62] </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=3rsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rsb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rsb RCSB], [http://www.ebi.ac.uk/pdbsum/3rsb PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/COBY_METJA COBY_METJA] Guanylyltransferase that catalyzes the synthesis of adenosylcobinamide-GDP (AdoCbi-GDP) from adenosylcobinamide-phosphate (AdoCbi-P) and GTP. Is involved in adenosylcobalamin biosynthesis. Binds one GTP per dimer. Can not use other NTPs or GDP. Does not display AdoCbi kinase activity. Is also able to catalyze the condensation of 2-phospho-L-lactate (LP) with GTP in vitro to form PPi and (2S)-lactyl-2-diphospho-5'-guanosine (LPPG), but is much less efficient than CofC, the presumed enzyme catalyzing this reaction in vivo.<ref>PMID:18260642</ref> <ref>PMID:19489548</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3rsb" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenosylcobinamide-phosphate guanylyltransferase]] | + | [[Category: Large Structures]] |
| | [[Category: Methanocaldococcus jannaschii]] | | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Escalante-Semerena, J C]] | + | [[Category: Escalante-Semerena JC]] |
| - | [[Category: Newmister, S A]] | + | [[Category: Newmister SA]] |
| - | [[Category: Otte, M M]] | + | [[Category: Otte MM]] |
| - | [[Category: Rayment, I]] | + | [[Category: Rayment I]] |
| - | [[Category: Pyrophosphorylase]]
| + | |
| - | [[Category: Pyrophosphorylase binding motif]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
COBY_METJA Guanylyltransferase that catalyzes the synthesis of adenosylcobinamide-GDP (AdoCbi-GDP) from adenosylcobinamide-phosphate (AdoCbi-P) and GTP. Is involved in adenosylcobalamin biosynthesis. Binds one GTP per dimer. Can not use other NTPs or GDP. Does not display AdoCbi kinase activity. Is also able to catalyze the condensation of 2-phospho-L-lactate (LP) with GTP in vitro to form PPi and (2S)-lactyl-2-diphospho-5'-guanosine (LPPG), but is much less efficient than CofC, the presumed enzyme catalyzing this reaction in vivo.[1] [2]
Publication Abstract from PubMed
In archaea and bacteria, the late steps in adenosylcobalamin (AdoCbl) biosynthesis are collectively known as the nucleotide loop assembly (NLA) pathway. In the archaeal and bacterial NLA pathways, two different guanylyltransferases catalyze the activation of the corrinoid. Structural and functional studies of the bifunctional bacterial guanylyltransferase that catalyze both ATP dependent corrinoid phosphorylation and GTP dependent guanylylation are available, but similar studies of the monofunctional archaeal enzyme that catalyzes only GTP dependent guanylylation are not. Herein, the three-dimensional crystal structure of the guanylyltransferase (CobY) enzyme from the archaeon Methanocaldococcus jannaschii (MjCobY)1 in complex with GTP is reported. The model identifies the location of the active site. An extensive mutational analysis was performed, and the functionality of the variant proteins was assessed in vivo and in vitro. Substitutions of residues Gly8, Gly153, or Asn177 resulted in >94% loss of catalytic activity, thus variant proteins failed to support AdoCbl synthesis in vivo. Results from isothermal titration calorimetry experiments showed that MjCobYG153D had 10-fold higher affinity for GTP than MjCobTWT, but failed to bind the corrinoid substrate. Results from Western blot analyses suggested that the above-mentioned substitutions render the protein unstable and prone to degradation; possible explanations for the observed instability of the variants are discussed within the framework of the three-dimensional crystal structure of MjCobYG153D in complex with GTP. The fold of MjCobY is strikingly similar to that of the N-terminal domain of Mycobacterium tuberculosis GlmU (MtbGlmU), a bifunctional acetyltransferase/uridyltransferase that catalyses the formation of uridine-diphosphate-N-acetylglucosamine (UDP-GlcNAc).
Structure and Mutational Analysis of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii: Insights into GTP Binding and Dimerization.,Newmister SA, Otte MM, Escalante-Semerena JC, Rayment I Biochemistry. 2011 May 4. PMID:21542645[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Grochowski LL, Xu H, White RH. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry. 2008 Mar 4;47(9):3033-7. doi: 10.1021/bi702475t. Epub 2008 Feb 9. PMID:18260642 doi:http://dx.doi.org/10.1021/bi702475t
- ↑ Otte MM, Escalante-Semerena JC. Biochemical characterization of the GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) enzyme of the hyperthermophilic archaeon Methanocaldococcus jannaschii. Biochemistry. 2009 Jun 30;48(25):5882-9. doi: 10.1021/bi8023114. PMID:19489548 doi:http://dx.doi.org/10.1021/bi8023114
- ↑ Newmister SA, Otte MM, Escalante-Semerena JC, Rayment I. Structure and Mutational Analysis of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii: Insights into GTP Binding and Dimerization. Biochemistry. 2011 May 4. PMID:21542645 doi:10.1021/bi200329t
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