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| | <StructureSection load='6q2d' size='340' side='right'caption='[[6q2d]], [[Resolution|resolution]] 3.45Å' scene=''> | | <StructureSection load='6q2d' size='340' side='right'caption='[[6q2d]], [[Resolution|resolution]] 3.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q2d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q2D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q2d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanobrevibacter_smithii Methanobrevibacter smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q2D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 3.45Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-(3-amino-3-carboxypropyl)histidine_synthase 2-(3-amino-3-carboxypropyl)histidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.108 2.5.1.108] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6q2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q2d OCA], [http://pdbe.org/6q2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q2d RCSB], [http://www.ebi.ac.uk/pdbsum/6q2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q2d ProSAT]</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=6q2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q2d OCA], [https://pdbe.org/6q2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q2d RCSB], [https://www.ebi.ac.uk/pdbsum/6q2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q2d ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A5UMY5_METS3 A5UMY5_METS3]] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967] [[http://www.uniprot.org/uniprot/A0A2H4U7K7_METSM A0A2H4U7K7_METSM]] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.[HAMAP-Rule:MF_00054][SAAS:SAAS00384500] | + | [https://www.uniprot.org/uniprot/A5UMY5_METS3 A5UMY5_METS3] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6q2d" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6q2d" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Elongation factor 3D structures|Elongation factor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dong, M]] | + | [[Category: Methanobrevibacter smithii]] |
| - | [[Category: Ealick, S E]] | + | [[Category: Dong M]] |
| - | [[Category: Fenwick, M K]]
| + | [[Category: Ealick SE]] |
| - | [[Category: Lin, H]] | + | [[Category: Fenwick MK]] |
| - | [[Category: Enzyme]] | + | [[Category: Lin H]] |
| - | [[Category: Iron sulfur cluster]] | + | |
| - | [[Category: Radical]]
| + | |
| - | [[Category: S-adenosylmethionine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
A5UMY5_METS3 Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).[PIRNR:PIRNR004967]
Publication Abstract from PubMed
Elongation factor 2 (EF-2), a five-domain, GTP-dependent ribosomal translocase of archaebacteria and eukaryotes, undergoes post-translational modification to form diphthamide on a specific histidine residue in domain IV prior to binding the ribosome. The first step of diphthamide biosynthesis in archaebacteria is catalyzed by Dph2, a homodimeric radical S-adenosylmethionine (SAM) enzyme having a noncanonical architecture. Here, we describe a 3.5 A resolution crystal structure of the Methanobrevibacter smithii (Ms) Dph2 homodimer bound to two molecules of MsEF-2, one of which is ordered and the other largely disordered. MsEF-2 is bound to both protomers of MsDph2, with domain IV bound to the active site of one protomer and domain III bound to a surface alpha-helix of an adjacent protomer. The histidine substrate of domain IV is inserted into the active site, which reveals for the first time the architecture of the Dph2 active site in complex with its target substrate. We also determined a high-resolution crystal structure of isolated MsDph2 bound to 5'-methylthioadenosine that shows a conserved arginine residue preoriented by conserved phenylalanine and aspartate residues for binding the carboxylate group of SAM. Mutagenesis experiments suggest that the arginine plays an important role in the first step of diphthamide biosynthesis.
The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.,Fenwick MK, Dong M, Lin H, Ealick SE Biochemistry. 2019 Oct 14. doi: 10.1021/acs.biochem.9b00718. PMID:31566354[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Fenwick MK, Dong M, Lin H, Ealick SE. The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis. Biochemistry. 2019 Oct 14. doi: 10.1021/acs.biochem.9b00718. PMID:31566354 doi:http://dx.doi.org/10.1021/acs.biochem.9b00718
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