Sandbox Reserved 309

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{{Template:Sandbox_Reserved_BCMB307}}
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{{STRUCTURE_2cdn|PDB=2cdn|SCENE=}}
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=Introduction/General Information=
=Introduction/General Information=
Adenylate kinase is a phosphotransferase that catalyzes the interconversion reaction of ATP, ADP, and AMP. It is part of the nucleotide and nucleoside kinases family. Its source is the Myobacterium tuberculosis bacterium. Since Adenylate Kinase is found to be essential for bacterial survival, it is targeted by drugs when treating the disease. <ref name=Bellinzoni>PMID: 16672241 </ref>
Adenylate kinase is a phosphotransferase that catalyzes the interconversion reaction of ATP, ADP, and AMP. It is part of the nucleotide and nucleoside kinases family. Its source is the Myobacterium tuberculosis bacterium. Since Adenylate Kinase is found to be essential for bacterial survival, it is targeted by drugs when treating the disease. <ref name=Bellinzoni>PMID: 16672241 </ref>
=Structure=
=Structure=
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Protein of 201 residues with a <scene name='Sandbox_Reserved_309/Ligand/1'>Ligand</scene>
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Protein of 201 residues with a <scene name='Sandbox_Reserved_309/Ligand/1'>Ligand</scene> consisting of two molecules of ADP (Adenosine-5'-Phosphate) and Magnesium ion.
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consisting of two molecules of ADP (Adenosine-5'-Phosphate) and Magnesium ion.
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==The solution structure==
==The solution structure==
With no ligand, is represented by a central CORE domain composed of a 5-stranded parallel beta sheet surrounded by 7 alpha helices, and two periferal domains, LID and NMP <ref name=Miron>PMID:14705932 </ref>
With no ligand, is represented by a central CORE domain composed of a 5-stranded parallel beta sheet surrounded by 7 alpha helices, and two periferal domains, LID and NMP <ref name=Miron>PMID:14705932 </ref>
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=Catalytic Mechanism=
=Catalytic Mechanism=
ADP+MgADP↔MgATP+AMP
ADP+MgADP↔MgATP+AMP
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=References=
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<Structure load=2cdn size='200' frame='true' align='left' caption= 'Adenosine-5'-Diphosphate and Mg' scene='Sandbox_Reserved_309/Ligand/1'/>
<Structure load=2cdn size='200' frame='true' align='left' caption= 'Adenosine-5'-Diphosphate and Mg' scene='Sandbox_Reserved_309/Ligand/1'/>
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Revision as of 02:19, 18 March 2011

This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

PDB ID 2cdn

Drag the structure with the mouse to rotate
2cdn, resolution 1.90Å ()
Ligands: ,
Activity: Adenylate kinase, with EC number 2.7.4.3
Related: 1p4s
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


Contents

Introduction/General Information

Adenylate kinase is a phosphotransferase that catalyzes the interconversion reaction of ATP, ADP, and AMP. It is part of the nucleotide and nucleoside kinases family. Its source is the Myobacterium tuberculosis bacterium. Since Adenylate Kinase is found to be essential for bacterial survival, it is targeted by drugs when treating the disease. [1]

Structure

Protein of 201 residues with a consisting of two molecules of ADP (Adenosine-5'-Phosphate) and Magnesium ion.

The solution structure

With no ligand, is represented by a central CORE domain composed of a 5-stranded parallel beta sheet surrounded by 7 alpha helices, and two periferal domains, LID and NMP [2]

The crystalline structure

Globular with a central core made by beta parallel sheet surrounded by alpha helices, a P-loop motif at the N-terminus that binds ATP, and two regions (LID and NMP). [1]

Function

Involved in nucleotide biosynthesis. Catalyzes the reversible Mg2+ dependent transfer of the terminal phosphate group from ATP to AMP releasing two molecules of ADP. LID and NMP binding regions go through a significant conformational change during the catalysis reaction depicted below. [1]

Catalytic Mechanism

ADP+MgADP↔MgATP+AMP

References

  1. ↑ 1.0 1.1 1.2 Bellinzoni M, Haouz A, Grana M, Munier-Lehmann H, Shepard W, Alzari PM. The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer. Protein Sci. 2006 Jun;15(6):1489-93. Epub 2006 May 2. PMID:16672241 doi:10.1110/ps.062163406
  2. ↑ Miron S, Munier-Lehmann H, Craescu CT. Structural and dynamic studies on ligand-free adenylate kinase from Mycobacterium tuberculosis revealed a closed conformation that can be related to the reduced catalytic activity. Biochemistry. 2004 Jan 13;43(1):67-77. PMID:14705932 doi:10.1021/bi0355995


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PDB ID 2cdn

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