8OOV

human NME-1 in complex with CoA

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-04-06 Released: 2023-06-07 
  • Deposition Author(s): Gouge, J., Hristov, H.D.
  • Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.

Tossounian, M.A.Hristov, S.D.Semelak, J.A.Yu, B.Y.K.Baczynska, M.Zhao, Y.Estrin, D.A.Trujillo, M.Filonenko, V.Gouge, J.Gout, I.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24119359
  • Primary Citation of Related Structures:  
    8OOV

  • PubMed Abstract: 

    Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3'-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.


  • Organizational Affiliation

    Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase A
A, B, C
172Homo sapiensMutation(s): 0 
Gene Names: NME1NDPKANM23
EC: 2.7.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P15531 (Homo sapiens)
Explore P15531 
Go to UniProtKB:  P15531
PHAROS:  P15531
GTEx:  ENSG00000239672 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15531
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.07α = 90
b = 113.012β = 90
c = 118.119γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom216404/A/19/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L010410/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S009027/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection