3gmt: Difference between revisions

Latest revision as of 09:55, 6 November 2024

Crystal structure of adenylate kinase from burkholderia pseudomallei

Structural highlights

3gmt is a 2 chain structure with sequence from Burkholderia pseudomallei 1710b. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	MSE, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAD_BURP1 Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity).

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

In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1A resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP(bd)) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 A. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state.

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state.,Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ Biochem Biophys Res Commun. 2010 Apr 16;394(4):1012-7. Epub 2010 Mar 21. PMID:20331978^[1]

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

References

↑ Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ. Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state. Biochem Biophys Res Commun. 2010 Apr 16;394(4):1012-7. Epub 2010 Mar 21. PMID:20331978 doi:10.1016/j.bbrc.2010.03.112

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ. Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state. Biochem Biophys Res Commun. 2010 Apr 16;394(4):1012-7. Epub 2010 Mar 21. PMID:20331978 doi:10.1016/j.bbrc.2010.03.112

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3gmt' size='340' side='right'caption='[[3gmt]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gmt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GMT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gmt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GMT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, BURPS1710b_1080 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=3gmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gmt OCA], [https://pdbe.org/3gmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gmt RCSB], [https://www.ebi.ac.uk/pdbsum/3gmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gmt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/KAD_BURP1 KAD_BURP1]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity).
+[https://www.uniprot.org/uniprot/KAD_BURP1 KAD_BURP1] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gm/3gmt_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>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Adenylate kinase]]
+[[Category: Burkholderia pseudomallei 1710b]]
-[[Category: Burp1]]
 [[Category: Large Structures]]
-[[Category: Abendroth, J]]
+[[Category: Abendroth J]]
-[[Category: Buchko, G W]]
+[[Category: Buchko GW]]
-[[Category: Hewitt, S N]]
+[[Category: Hewitt SN]]
-[[Category: Myler, P J]]
+[[Category: Myler PJ]]
-[[Category: Napuli, A J]]
+[[Category: Napuli AJ]]
-[[Category: Robinson, H]]
+[[Category: Robinson H]]
-[[Category: Structural genomic]]
+[[Category: Stacy R]]
-[[Category: Stacy, R]]
+[[Category: Staker BL]]
-[[Category: Staker, B L]]
+[[Category: Stewart L]]
-[[Category: Stewart, L]]
+[[Category: Van Voorhis W]]
-[[Category: Voorhis, W Van]]
-[[Category: Atp-binding]]
-[[Category: Burkholderia pseudomallei]]
-[[Category: Kinase]]
-[[Category: Nucleotide biosynthesis]]
-[[Category: Nucleotide-binding]]
-[[Category: Ssgcid]]
-[[Category: Transferase]]

3gmt: Difference between revisions

Latest revision as of 09:55, 6 November 2024

Crystal structure of adenylate kinase from burkholderia pseudomallei

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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