5cb5: Difference between revisions

Latest revision as of 16:07, 8 November 2023

Structural Insights into the Mechanism of Escherichia coli Ymdb

Structural highlights

5cb5 is a 18 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	ACT, APR, SO4, ZOD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YMDB_ECOLI Deacetylates O-acetyl-ADP ribose. Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation.^[1] ^[2]

Publication Abstract from PubMed

The Escherichia coli protein YmdB belongs to the macrodomain protein family, which can bind ADP-ribose (ADPr) and its derivatives. Recently, YmdB was reported to be capable of deacetylating O-acetyl-ADP-ribose (OAADPr) to yield ADPr and free acetate. To study the substrate specificity and catalytic mechanism, the crystal structures of E. coli YmdB in complex with ADPr, double mutant N25AD35A complexed with 2'-OAADPr, and Y126A/ADPr complex were solved at 1.8A, 2.8A and 3.0A resolution, respectively. Structural and biochemical studies reveal that YmdB has substrate specificity against 2'-OAADPr. The conserved residues Asn25 and Asp35 are crucial for catalytic activity, and an active water molecule is proposed as the nucleophile to attack the acetyl group of 2'-OAADPr. Our findings indicate that the conserved phenyl group of Tyr126 plays a crucial role in catalytic activity by stabilizing the right orientation of distal ribose and that Gly32 may be important for activity by interacting with the acetyl group of 2'-OAADPr. Based on these observations, a model of YmdB in complex with 2'-OAADPr was made to illustrate the proposed catalytic mechanism of YmdB.

Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase.,Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kim KS, Manasherob R, Cohen SN. YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity. Genes Dev. 2008 Dec 15;22(24):3497-508. doi: 10.1101/gad.1729508. PMID:19141481 doi:https://dx.doi.org/10.1101/gad.1729508
↑ Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O, Denu JM, Ahel I. Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem. 2011 Apr 15;286(15):13261-71. Epub 2011 Jan 21. PMID:21257746 doi:10.1074/jbc.M110.206771
↑ Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J. Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase. J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419 doi:https://dx.doi.org/10.1016/j.jsb.2015.10.010

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OCA

[1] Kim KS, Manasherob R, Cohen SN. YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity. Genes Dev. 2008 Dec 15;22(24):3497-508. doi: 10.1101/gad.1729508. PMID:19141481 doi:https://dx.doi.org/10.1101/gad.1729508

[2] Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O, Denu JM, Ahel I. Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem. 2011 Apr 15;286(15):13261-71. Epub 2011 Jan 21. PMID:21257746 doi:10.1074/jbc.M110.206771

[3] Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J. Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase. J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419 doi:https://dx.doi.org/10.1016/j.jsb.2015.10.010

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[5cb5]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CB5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZOD:[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXYMETHYL]-2,4-BIS(OXIDANYL)OXOLAN-3-YL]+ETHANOATE'>ZOD</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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZOD:[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXYMETHYL]-2,4-BIS(OXIDANYL)OXOLAN-3-YL]+ETHANOATE'>ZOD</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=5cb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cb5 OCA], [https://pdbe.org/5cb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cb5 RCSB], [https://www.ebi.ac.uk/pdbsum/5cb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cb5 ProSAT]</span></td></tr>
 </table>

5cb5: Difference between revisions

Latest revision as of 16:07, 8 November 2023

Structural Insights into the Mechanism of Escherichia coli Ymdb

Structural highlights

Function

Publication Abstract from PubMed

References

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