1c9k

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[[Image:1c9k.gif|left|200px]]<br /><applet load="1c9k" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1c9k, resolution 2.2&Aring;" />
 
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'''THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE'''<br />
 
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==Overview==
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==THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE==
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The X-ray crystal structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) from Salmonella typhimurium bound to GMP has been determined by molecular replacement to 2.2 A resolution. CobU is a bifunctional enzyme, which catalyzes the phosphorylation of the 1-amino-O-2-propanol side chain of the adenosylcobinamide ring and subsequently functions as a guanylyltransferase to form adenosylcobinamide.GDP. The transferase activity involves a covalent enzyme-guanylyl intermediate that is most likely a phosphoramidate linkage to His(46). Previous studies have shown that the enzyme is a homotrimer and adopts a pinwheel shape. Each subunit consists of a single domain of six parallel beta-strands and one antiparallel strand flanked on either side by a total of five alpha-helices and one helical turn. Interestingly, His(46) in the apoenzyme is located a considerable distance from the kinase active site or P-loop motif and is solvent-exposed [Thompson, T. B., et al. (1998) Biochemistry 37, 7686-7695]. To examine the structural relationship of the two active sites, CobU was cocrystallized with GTP and pyrophosphate. Crystals belong to space group P2(1)2(1)2(1) with the following unit cell dimensions: a = 58. 4 A, b = 87.8 A, and c = 101.6 A. The structure shows electron density for the hydrolysis product GMP rather than the expected covalent guanylyl intermediate which appears to have been hydrolyzed in the crystal lattice. Even so, CobU exhibits a substantial conformational rearrangement. The helix axis containing His(46), the site of guanylylation, rotates 30 degrees and translates 11 A relative to the apo structure and is accompanied by compensatory unwinding and rewinding at the helix ends to allow the induction of a guanosine binding pocket between beta-strand 2 and alpha-helix 2. This conformational change brings the C(alpha) of His(46) approximately 10 A closer to the P-loop motif such that a phosphate ion located in the P-loop is only 6 A from the alpha-phosphate of GMP. This suggests that the P-loop motif may be used to coordinate the terminal phosphates in both the transferase and kinase reactions and implies that the active sites for both reactions overlap.
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<StructureSection load='1c9k' size='340' side='right'caption='[[1c9k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1c9k]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C9K FirstGlance]. <br>
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1C9K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=5GP:'>5GP</scene> and <scene name='pdbligand=POP:'>POP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C9K OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c9k OCA], [https://pdbe.org/1c9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c9k RCSB], [https://www.ebi.ac.uk/pdbsum/1c9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c9k ProSAT]</span></td></tr>
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Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site., Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I, Biochemistry. 1999 Oct 5;38(40):12995-3005. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10529169 10529169]
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</table>
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[[Category: Salmonella typhimurium]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/COBU_SALTY COBU_SALTY] Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate.
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[[Category: Esclante-Semerena, J C.]]
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== Evolutionary Conservation ==
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[[Category: Rayment, I.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Thomas, M G.]]
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Check<jmol>
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[[Category: Thompson, T B.]]
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<jmolCheckbox>
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[[Category: 5GP]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/1c9k_consurf.spt"</scriptWhenChecked>
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[[Category: MG]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: PO4]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: POP]]
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</jmolCheckbox>
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[[Category: alpha/beta structure rossmann fold p-loop]]
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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=1c9k ConSurf].
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[[Category: transferase]]
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<div style="clear:both"></div>
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__TOC__
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:03:49 2008''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
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[[Category: Esclante-Semerena JC]]
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[[Category: Rayment I]]
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[[Category: Thomas MG]]
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[[Category: Thompson TB]]

Current revision

THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE

PDB ID 1c9k

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