Related Experiment Video

Updated: Jul 11, 2026

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit
22:10

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

Published on: June 28, 2013

Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae

G Obmolova1, A Teplyakov, N Bonander

  • 1Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

Journal of Structural Biology
|March 12, 2002
PubMed

Insights

Dephospho-coenzyme A kinase, crucial for CoA biosynthesis, was structurally analyzed. Its three-domain structure and ATP-binding site reveal insights into the enzyme

Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Dephospho-coenzyme A (CoA) kinase catalyzes the terminal phosphorylation step in CoA biosynthesis.
  • This reaction utilizes ATP as the phosphate donor to phosphorylate the 3'-hydroxyl group of ribose.
  • Understanding the structure of this enzyme is key to elucidating CoA metabolic pathways.

Purpose of the Study:

  • To determine the crystal structure of Haemophilus influenzae dephospho-CoA kinase.
  • To elucidate the substrate-binding site and catalytic mechanism.
  • To compare the structure with other known nucleotide kinases.

Main Methods:

  • Cloning and expression of the Haemophilus influenzae dephospho-CoA kinase gene.
  • X-ray crystallography to determine the enzyme's structure at 2.0-A resolution.
  • Structural analysis of the enzyme in complex with ATP.

Main Results:

  • The crystal structure reveals a three-domain protein: nucleotide-binding, substrate-binding, and lid domains.
  • ATP binds to the canonical P-loop, similar to other kinases.
  • An unusual double-pocket structure at the CoA-binding site, located at the interface of all three domains, was identified, along with key residues for catalysis.

Conclusions:

  • The elucidated structure provides atomic-level insights into dephospho-CoA kinase function.
  • The unique substrate-binding site suggests specific adaptations for CoA phosphorylation.
  • Structural analysis indicates potential large domain movements during the catalytic cycle.

More Related Videos

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD13:34

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α11:27

A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α

Published on: November 2, 2018

Related Concept Videos

Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
ATP Synthase: Mechanism01:48

ATP Synthase: Mechanism

In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased ATP...
ATP Synthase: Structure01:18

ATP Synthase: Structure

ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
Pinching-off of Coated Vesicles01:32

Pinching-off of Coated Vesicles

Vesicle budding is orchestrated by distinct cytosolic proteins such as adaptor proteins, coat proteins, and GTPases. To initiate vesicle budding, membrane-bending proteins containing crescent-shaped BAR domains bind to the lipid heads in the bilayer and distort the membrane to form a protein-coated vesicle bud. Adaptors proteins such as AP2 for clathrin-coated vesicles can nucleate on the deformed membrane. Finally, coat proteins such as clathrin or COPI and COPII assemble into a coat forming...
Structure of Cadherins01:25

Structure of Cadherins

The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This diversity of cadherins...