1s5p

From Proteopedia

(Difference between revisions)

Current revision

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.

Structural highlights

1s5p is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.96Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NPD_ECOLI NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Activates the enzyme acetyl-CoA synthetase by deacetylating 'Lys-609' in the inactive, acetylated form of the enzyme. May also modulate the activity of other propionyl-adenosine monophosphate (AMP)-forming enzymes.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Sirtuins are NAD+-dependent protein deacetylase enzymes that are broadly conserved from bacteria to human, and have been implicated to play important roles in gene regulation, metabolism and longevity. cobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase (Acs) at an active site lysine to stimulate its enzymatic activity. Here, we report the structure of cobB bound to an acetyl-lysine containing non-cognate histone H4 substrate. A comparison with the previously reported archaeal and eukaryotic sirtuin structures reveals the greatest variability in a small zinc-binding domain implicated to play a particularly important role in substrate-specific binding by the sirtuin proteins. Comparison of the cobB/histone H4 complex with other sirtuin proteins in complex with acetyl-lysine containing substrates, further suggests that contacts to the acetyl-lysine side-chain and beta-sheet interactions with residues directly C-terminal to the acetyl-lysine represent conserved features of sirtuin-substrate recognition. Isothermal titration calorimetry studies were used to compare the affinity of cobB for a variety of cognate and non-cognate acetyl-lysine-bearing peptides revealing an exothermic reaction with relatively little discrimination between substrates. In contrast, similar studies employing intact acetylated Acs protein as a substrate reveal a binding reaction that is endothermic, suggesting that cobB recognition of substrate involves a burial of hydrophobic surface and/or structural rearrangement involving substrate regions distal to the acetyl-lysine-binding site. Together, these studies suggest that substrate-specific binding by sirtuin proteins involves contributions from the zinc-binding domain of the enzyme and substrate regions distal to the acetyl-lysine-binding site.

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli.,Zhao K, Chai X, Marmorstein R J Mol Biol. 2004 Mar 26;337(3):731-41. PMID:15019790^[4]

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

References

↑ Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A. 2000 May 23;97(11):5807-11. PMID:10811920 doi:http://dx.doi.org/10.1073/pnas.110148297
↑ Colak G, Xie Z, Zhu AY, Dai L, Lu Z, Zhang Y, Wan X, Chen Y, Cha YH, Lin H, Zhao Y, Tan M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics. 2013 Dec;12(12):3509-20. doi: 10.1074/mcp.M113.031567. Epub , 2013 Oct 31. PMID:24176774 doi:http://dx.doi.org/10.1074/mcp.M113.031567
↑ Zhao K, Chai X, Marmorstein R. Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli. J Mol Biol. 2004 Mar 26;337(3):731-41. PMID:15019790 doi:10.1016/j.jmb.2004.01.060
↑ Zhao K, Chai X, Marmorstein R. Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli. J Mol Biol. 2004 Mar 26;337(3):731-41. PMID:15019790 doi:10.1016/j.jmb.2004.01.060

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1s5p"

Categories: Escherichia coli | Large Structures | Chai X | Marmorstein R | Zhao K

@@ Line 1: / Line 1: @@
 ==Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.==
-<StructureSection load='1s5p' size='340' side='right' caption='[[1s5p]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+<StructureSection load='1s5p' size='340' side='right'caption='[[1s5p]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1s5p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S5P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1s5p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S5P FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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]] 1.96&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NPDA, COBB, B1120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s5p OCA], [https://pdbe.org/1s5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s5p RCSB], [https://www.ebi.ac.uk/pdbsum/1s5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s5p ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s5p RCSB], [http://www.ebi.ac.uk/pdbsum/1s5p PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/NPD_ECOLI NPD_ECOLI] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Activates the enzyme acetyl-CoA synthetase by deacetylating 'Lys-609' in the inactive, acetylated form of the enzyme. May also modulate the activity of other propionyl-adenosine monophosphate (AMP)-forming enzymes.<ref>PMID:10811920</ref> <ref>PMID:24176774</ref> <ref>PMID:15019790</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s5/1s5p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s5/1s5p_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1s5p ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1s5p" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 31: / Line 34: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Chai, X.]]
+[[Category: Large Structures]]
-[[Category: Marmorstein, R.]]
+[[Category: Chai X]]
-[[Category: Zhao, K.]]
+[[Category: Marmorstein R]]
-[[Category: Hydrolase]]
+[[Category: Zhao K]]
-[[Category: Protein deacetylase]]
-[[Category: Sir2 homologue]]

1s5p

From Proteopedia

Current revision

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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