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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.

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Contents 1 Introduction/General Information 2 Structure= 2.1 The solution structure 2.2 The crystalline structure 3 Function 4 Catalytic Mechanism 5 references

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.

Structure=

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

spinqualitylabelsall models PDB ID 2cdn Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 ^[1]

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).

spinqualitylabelsall models PDB ID 2cdn Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2cdn, resolution 1.90Å ()
Ligands:	,
Activity:	Adenylate kinase, with EC number 2.7.4.3
Related:	1p4s
Structural annotation: Resources: CATH : 2Cdna00 InterPro : Ipr000850, Ipr006259, Ipr011769 Pfam : PF00406 UniProt : P69440
Functional annotation: Cellular component: cytoplasm Biological process: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process nucleotide biosynthetic process Molecular function: nucleotide kinase activity adenylate kinase activity transferase activity ATP binding phosphotransferase activity, phosphate group as acceptor nucleotide binding kinase activity
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, PDBsum, RCSB
Coordinates:	save as pdb, mmCIF, xml

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.

Catalytic Mechanism

ADP+MgADP↔MgATP+AMP

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references

1. ↑ 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