Macromolecule Content

• Total Structure Weight: 20269.80 
• Atom Count: 1415 
• Residue Count: 185 
• Unique protein chains: 1

2KMV

Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-free form

• DOI: 10.2210/pdb2KMV/pdb
• BMRB: 16440

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-08-05 Released: 2009-12-01 
• Deposition Author(s): Banci, L., Bertini, I., Cantini, F., Inagaki, S., Migliardi, M., Rosato, A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

The binding mode of ATP revealed by the solution structure of the N-domain of human ATP7A.

Banci, L., Bertini, I., Cantini, F., Inagaki, S., Migliardi, M., Rosato, A.

(2009) J.Biol.Chem. --: --

• PubMed: 19917612 
• DOI: 10.1074/jbc.M109.054262
• Primary Citation of Related Structures:  
  2KMX


• PubMed Abstract: 
  

We report the solution NMR structures of the N-domain of the Menkes protein (ATP7A) in the ATP-free and ATP-bound forms. The structures consist of a twisted antiparallel six-stranded beta-sheet flanked by two pairs of alpha-helices. A protein loop of 50 amino acids located between beta 3 and beta 4 is disordered and mobile on the subnanosecond time scale. ATP binds with an affinity constant of (1.2 +/- 0.1) x 10(4) m(-1) and exchanges with a rate of the order of 1 x 10(3) s(-1). The ATP-binding cavity is considerably affected by the presence of the ligand, resulting in a more compact conformation in the ATP-bound than in the ATP-free form. This structural variation is due to the movement of the alpha1-alpha2 and beta2-beta 3 loops, both of which are highly conserved in copper(I)-transporting P(IB)-type ATPases. The present structure reveals a characteristic binding mode of ATP within the protein scaffold of the copper(I)-transporting P(IB)-type ATPases with respect to the other P-type ATPases. In particular, the binding cavity contains mainly hydrophobic aliphatic residues, which are involved in van der Waal's interactions with the adenine ring of ATP, and a Glu side chain, which forms a crucial hydrogen bond to the amino group of ATP.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Copper-transporting ATPase 1	A	185	Homo sapiens	Mutation(s): 0  Gene Names: ATP7A (MC1, MNK) EC: 7.2.2.8
Find proteins for Q04656 (Homo sapiens) Go to Gene View: ATP7A Go to UniProtKB:  Q04656

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• Olderado: 2KMV Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-05 
• Released Date: 2009-12-01 
• Deposition Author(s): Banci, L., Bertini, I., Cantini, F., Inagaki, S., Migliardi, M., Rosato, A.

Revision History 

• Version 1.0: 2009-12-01
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance