View source for 8ykc


==Crystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase complexed with GDP==
<StructureSection load='8ykc' size='340' side='right'caption='[[8ykc]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8ykc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylocapsa_palsarum Methylocapsa palsarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8YKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YKC 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]] 1.921&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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=8ykc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ykc OCA], [https://pdbe.org/8ykc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ykc RCSB], [https://www.ebi.ac.uk/pdbsum/8ykc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ykc ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A1I3YTB1_9HYPH A0A1I3YTB1_9HYPH] Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate.[ARBA:ARBA00003889][PIRNR:PIRNR006135]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) is one of the key enzymes that participate in the biosynthesis of cobalamin, specifically lining the lower ligand 5,6-dimethylbenzimidazole in the alpha-position of cyclic tetrapyrrolidine. During this process, CobU exhibits two distinct activities: kinase and nucleotidyl transferase, using two nucleoside triphosphates. A structural study of CobU from Salmonella typhimurium showed that guanosine triphosphate binding induces a conformational rearrangement of helix 2. This rearrangement decreases the distance between the phosphate binding loop (P-loop) and helix 2, which is important for the subsequent guanylylation step of the reaction. However, these findings provide only partial insights into the mechanism of CobU at the structural level, and the precise molecular details of this mechanism have not yet been studied. As a first step towards elucidating the molecular mechanisms and sequence of events involved in the phosphorylation and guanylylation steps, we report the high-resolution crystal structures of phosphorylated -MpaCobU (1.8 A), the C91S mutant (1.5 A), the guanosine diphosphate complex (1.9 A), and the adenosylcobinamide-phosphate complex (2.6 A) from Methylocapsa palsarum for the first time. High-resolution structures revealed the crucial elements governing the catalytic steps of MpaCobU, thereby contributing to understanding the catalytic mechanism of CobU at the molecular level.

A structure-based mechanism of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (MpaCobU) from Methylocapsa palsarum.,Nam Y, Ahn YY, Kim BM, Kim K, Lee JH, Do H Int J Biol Macromol. 2024 Sep 24;280(Pt 3):136021. doi: , 10.1016/j.ijbiomac.2024.136021. PMID:39326622<ref>PMID:39326622</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8ykc" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Methylocapsa palsarum]]
[[Category: Do H]]
[[Category: Nam Y]]