Adenylate kinase: Difference between revisions

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Alexander Berchansky, Michal Harel

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-[[Image:3l0p.jpg|left|200px|thumb|Crystal Structure of Adenylate kinase [[3l0p]]]]
+<StructureSection load="" size="350" color=""   spin="on" Scene ="Journal:JBIC:1/Jbic1_opening/2" caption="(PDB code [[3l0p]]) Crystal structure of Fe (orange) bound adenylate kinase complex with glycerol from ''Desulfovibrio gigas''">
-{{STRUCTURE_3l0p|  PDB=3l0p  | SIZE=300| SCENE= |right|CAPTION=Adenylate kinase [[3l0p]] }}
-[[Adenylate kinase]] (ADK) is a phosphotransferase which catalyzes the interconversion of ADP to ATP+AMP.  ADK is important in cellular energy homeostasis. The images at the left and at the right correspond to one representative ADK, ''i.e.'' the crystal structure of Adenylate kinase from ''Desulfovibrio gigas'' ([[3l0p]]).
+[[Adenylate kinase]] (ADK, EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3]) is a [[Phosphotransferase]] which catalyzes the interconversion of ADP to ATP+AMP.  ADK is important in cellular energy homeostasis. Dinucleotides polyphosphates like diadenosine pentaphosphate
+(AP5) inhibit ADK.
-{{TOC limit|limit=2}}
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adenylate kinase is an essential catalyst for cellular growth and multiplication. ADK belongs to a family of enzymes essential to life, and is highly abundant inside the cell. It is involved in the reversible transfer of the terminal phosphate group from Mg2+ATP to Mg2+AMP with high energy turnover: Mg2+ATP + AMP&#8596;Mg2+ADP + ADP.
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+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adenylate kinases (ADK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, <scene name='Journal:JBIC:1/Metal_bound/4'>three metal ions</scene>, zinc, cobalt and iron, have been found in ADK from Gram-negative bacteria. Crystal structures of substrate-free ADK from Desulfovibrio gigas with three different metal ions: <scene name='Journal:JBIC:1/Zinc_bound/3'>Zn2+, Zn-ADK</scene> ([[2xb4]]); <scene name='Journal:JBIC:1/Cobalt_bound/7'>Co2+, Co-ADK</scene> ([[3l0s]]) and <scene name='Journal:JBIC:1/Fe_bound/8'>Fe2+, Fe-ADK</scene> ([[3l0p]]) bound in its LID domain have been determined by X-ray crystallography. 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.
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+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The structures of Zn- , Co- and Fe-ADK contain the <scene name='Journal:JBIC:1/Lid_domain/5'>characteristic LID domain (residues 125-163)</scene> and <scene name='Journal:JBIC:1/Core_domain/1'>Core (residues 1-124 and 164-223) domains</scene>, which also include the AMP binding region. The LID domain harbors the <scene name='Journal:JBIC:1/Metal_motif/1'>Cys129-X5-His135-X15-Cys151-X2-Cys154- motif</scene>, which is responsible for metal binding in a tetrahedral fashion. In the absence of any substrate, the LID domain of all holo forms of ADK was present in a fully open conformational state. The Core domain is <scene name='Journal:JBIC:1/Core_connection/3'>connected to the LID by residues 116-123 and 165-173</scene>. This Core domain mainly consists of a <scene name='Journal:JBIC:1/Core_helix/3'>five stranded beta sheet surrounded by 5 helices</scene> that keep the integrity of the tertiary structure of the enzyme. A <scene name='Journal:JBIC:1/Walker/4'>Walker motif</scene> with conserved sequence; <span style="color:#FF0000">G</span>-<span style="color:#FF8040">X</span>-<span style="color:#FFFF00">X</span>-<span style="color:#00FF00">G</span>-<span style="color:#0000FF">X</span>-<span style="color:#FF00FF">G</span>-<span style="color:#00FFFF">K</span> is present in the N-terminal region. The structures presented herein further reinforce the notion that the metal ion is purely structural, contributing to the stability of the LID domain.<ref >DOI 10.1007/s00775-010-0700-8</ref>
 == 3D Structures of Adenylate kinase ==
+[[Adenylate kinase 3D structures]]
+</StructureSection>
-[[3l0p]] – DgADK+Fe – ''Desulfovibrio gigas''<br />
+==References==
-[[3l0s]] – DgADK+Co<br />
+<references/>
-[[2xb4]] – DgADK+Zn<br />
-[[3hpq]], [[3hpr]], [[1e4v]], [[1e4y]] – EcADK (mutant)+AP5 – ''Escherichia coli''<br />
-[[4ake]] – EcADK<br />
-[[1ank]] – EcADK+AMP+AMPPNP<br />
-[[1ake]] – EcADK+AP5<br />
-[[3h86]] – ADK+AP5 – ''Methanococcus maripaludis''<br />
-[[3fb4]] – ADK+Zn+AP5 – ''Marinibacillus marinus''<br />
-[[3dkv]], [[3dl0]], [[1p3j]] - BsADK+Zn+AP5 – ''Bacillus subtilis''<br />
-[[2qaj]], [[2oo7]], [[2p3s]], [[2ori]], [[2osb]], [[2eu8]] – BsADK (mutant)+Zn+AP5<br />
-[[3gmt]] – ADK – ''Burkholderia pseudodomallei''<br />
-[[3cm0]] – ADK – ''Thermus thermophilus''<br />
-[[2rgx]] - AaADK+Zn+AP5 – ''Aquifex aeolicus''<br />
-[[2rh5]] – AaADK<br />
-[[3be4]] – ADK+AP5 – ''Cryptosporidium parvum''<br />
-[[2cdn]] – MtADK+ADP – ''Mycobacterium tuberculosis''<br />
-[[1p4s]] - MtADK<br />
-[[2c9y]] – hADK 2+bis-adenosine tetraphosphate – human<br />
-[[2ar7]] – hADK 4<br />
-[[2bbw]] – hADK 4+diguanosine pentaphosphate<br />
-[[2bwj]] – hADK 5+AMP<br />
-[[1s3g]] - ADK+Zn+AP5 – ''Bacillus globisporus''<br />
-[[1kht]] – ADK+AMP – ''Methanococcus voltae''<br />
-[[1ki9]] – ADK – ''Methanococcus thermolithotrophicus''<br />
-[[1nks]] – ADK+AMP+ADP – ''Sulfolobus acidocaldarius''<br />
-[[1zak]] – ADK+AP5 – maize<br />
-[[1zip]], [[1zin]] – ADK+Zn+Mn+AP5 – ''Bacillus stearothermophilus''<br />
-[[1ak2]], [[2ak2]] – bADK – bovine<br />
-[[2ak3]] – bADK+AMP<br />
-[[1dvr]] – yADK (mutant)+ATP analog – yeast<br />
-[[1aky]], [[2aky]] – yADK+AP5<br />
-[[3aky]] - yADK (mutant)+AP5<br />
-[[3adk]] – ADK - pig<br />
 [[Category:Topic Page]]