2mzb: Difference between revisions

Revision as of 08:11, 8 March 2023

Solution structural studies of GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) from Methanocaldococcus jannaschii

Structural highlights

2mzb is a 1 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

GTP:adenosylcobinamide-phosphate (AdoCbi-P) guanylyl transferase (CobY) is an enzyme that transfers the GMP moiety of GTP to AdoCbi yielding AdoCbi-GDP in the late steps of the assembly of Ado-cobamides in archaea. The failure of repeated attempts to crystallize ligand-free (apo) CobY prompted us to explore its 3D structure by solution NMR spectroscopy. As reported here, the solution structure has a mixed alpha/beta fold consisting of seven beta-strands and five alpha-helices, which is very similar to a Rossmann fold. Titration of apo-CobY with GTP resulted in large changes in amide proton chemical shifts that indicated major structural perturbations upon complex formation. However, the CobY:GTP complex as followed by 1H-15N HSQC spectra was found to be unstable over time: GTP hydrolyzed and the protein converted slowly to a species with an NMR spectrum similar to that of apo-CobY. The variant CobYG153D, whose GTP complex was studied by X-ray crystallography, yielded NMR spectra similar to those of wild-type CobY in both its apo- state and in complex with GTP. The CobYG153D:GTP complex was also found to be unstable over time.

Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii.,Singarapu KK, Otte MM, Tonelli M, Westler WM, Escalante-Semerena JC, Markley JL PLoS One. 2015 Oct 29;10(10):e0141297. doi: 10.1371/journal.pone.0141297., eCollection 2015. PMID:26513744^[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:https://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:https://dx.doi.org/10.1021/bi8023114
↑ Singarapu KK, Otte MM, Tonelli M, Westler WM, Escalante-Semerena JC, Markley JL. Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii. PLoS One. 2015 Oct 29;10(10):e0141297. doi: 10.1371/journal.pone.0141297., eCollection 2015. PMID:26513744 doi:https://dx.doi.org/10.1371/journal.pone.0141297

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1021/bi702475t

[2] 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:https://dx.doi.org/10.1021/bi8023114

[3] Singarapu KK, Otte MM, Tonelli M, Westler WM, Escalante-Semerena JC, Markley JL. Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii. PLoS One. 2015 Oct 29;10(10):e0141297. doi: 10.1371/journal.pone.0141297., eCollection 2015. PMID:26513744 doi:https://dx.doi.org/10.1371/journal.pone.0141297

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Solution structural studies of GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) from Methanocaldococcus jannaschii==
-<StructureSection load='2mzb' size='340' side='right'caption='[[2mzb]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2mzb' size='340' side='right'caption='[[2mzb]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2mzb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metja Metja]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MZB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2mzb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MZB FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cobY, MJ1117 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>
+</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=2mzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mzb OCA], [https://pdbe.org/2mzb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mzb RCSB], [https://www.ebi.ac.uk/pdbsum/2mzb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mzb ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosylcobinamide-phosphate_guanylyltransferase Adenosylcobinamide-phosphate guanylyltransferase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2mzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mzb OCA], [https://pdbe.org/2mzb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mzb RCSB], [https://www.ebi.ac.uk/pdbsum/2mzb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mzb ProSAT]</span></td></tr>
 </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>
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Adenosylcobinamide-phosphate guanylyltransferase]]
 [[Category: Large Structures]]
-[[Category: Metja]]
+[[Category: Methanocaldococcus jannaschii DSM 2661]]
-[[Category: Escalante-Semerena, J C]]
+[[Category: Escalante-Semerena JC]]
-[[Category: Markley, J L]]
+[[Category: Markley JL]]
-[[Category: Otte, M]]
+[[Category: Otte M]]
-[[Category: Singarapu, K]]
+[[Category: Singarapu K]]
-[[Category: Tonelli, M]]
+[[Category: Tonelli M]]
-[[Category: Westler, W M]]
+[[Category: Westler WM]]
-[[Category: Transferase]]

2mzb: Difference between revisions

Revision as of 08:11, 8 March 2023

Solution structural studies of GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) from Methanocaldococcus jannaschii

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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