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==Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas==
==Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas==
<StructureSection load='3l0s' size='340' side='right' caption='[[3l0s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3l0s' size='340' side='right'caption='[[3l0s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3l0s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L0S FirstGlance]. <br>
<table><tr><td colspan='2'>[[3l0s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L0S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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=3l0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l0s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l0s RCSB], [http://www.ebi.ac.uk/pdbsum/3l0s PDBsum]</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=3l0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l0s OCA], [https://pdbe.org/3l0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l0s RCSB], [https://www.ebi.ac.uk/pdbsum/3l0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l0s ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/C7U112_DESGI C7U112_DESGI]] 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).[HAMAP-Rule:MF_00235]  
[https://www.uniprot.org/uniprot/C7U112_MEGGA C7U112_MEGGA] 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.[HAMAP-Rule:MF_00235]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 A, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.
 
Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria.,Mukhopadhyay A, Kladova AV, Bursakov SA, Gavel OY, Calvete JJ, Shnyrov VL, Moura I, Moura JJ, Romao MJ, Trincao J J Biol Inorg Chem. 2010 Sep 7. PMID:20821240<ref>PMID:20821240</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Adenylate kinase|Adenylate kinase]]
*[[Adenylate kinase|Adenylate kinase]]
*[[Journal:JBIC:1|Journal:JBIC:1]]
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Adenylate kinase]]
[[Category: Large Structures]]
[[Category: Atcc 19364]]
[[Category: Megalodesulfovibrio gigas]]
[[Category: Mukhopadhyay, A]]
[[Category: Mukhopadhyay A]]
[[Category: Romao, M J]]
[[Category: Romao MJ]]
[[Category: Trincao, J]]
[[Category: Trincao J]]
[[Category: Atp-binding]]
[[Category: Cobalt]]
[[Category: Gram-negative]]
[[Category: Kinase]]
[[Category: Nucleotide-binding]]
[[Category: Transferase]]

Latest revision as of 11:30, 20 March 2024

Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigasCrystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas

Structural highlights

3l0s is a 2 chain structure with sequence from Megalodesulfovibrio gigas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C7U112_MEGGA 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.[HAMAP-Rule:MF_00235]

See Also

3l0s, resolution 2.00Å

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