6CKM

N. meningitidis CMP-sialic acid synthetase in the presence of CMP-sialic acid and Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Catalytic Cycle ofNeisseria meningitidisCMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography.

Matthews, M.M.McArthur, J.B.Li, Y.Yu, H.Chen, X.Fisher, A.J.

(2019) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.9b00517
  • Primary Citation of Related Structures:  
    6CKJ, 6CKK, 6CKL, 6CKM

  • PubMed Abstract: 

    Cytidine 5'-monophosphate (CMP)-sialic acid synthetase (CSS) is an essential enzyme involved in the biosynthesis of carbohydrates and glycoconjugates containing sialic acids, a class of α-keto acids that are generally terminal key recognition residues by many proteins that play important biological and pathological roles. The CSS from Neisseria meningitidis (NmCSS) has been commonly used with other enzymes such as sialic acid aldolase and/or sialyltransferase in synthesizing a diverse array of compounds containing sialic acid or its naturally occurring and non-natural derivatives. To better understand its catalytic mechanism and substrate promiscuity, four NmCSS crystal structures trapped at various stages of the catalytic cycle with bound substrates, substrate analogues, and products have been obtained and are presented here. These structures suggest a mechanism for an "open" and "closed" conformational transition that occurs as sialic acid binds to the NmCSS/cytidine-5'-triphosphate (CTP) complex. The closed conformation positions critical residues to help facilitate the nucleophilic attack of sialic acid C2-OH to the α-phosphate of CTP, which is also aided by two observed divalent cations. Product formation drives the active site opening, promoting the release of products.


  • Organizational Affiliation

    Department of Chemistry, University of California, Davis, California 95616, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylneuraminate cytidylyltransferase228Neisseria meningitidisMutation(s): 0 
Gene Names: neuAsiaBsynB
EC: 2.7.7.43
UniProt
Find proteins for P0A0Z8 (Neisseria meningitidis)
Explore P0A0Z8 
Go to UniProtKB:  P0A0Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0Z8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.372α = 90
b = 156.02β = 90
c = 38.714γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI130684

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2020-03-18
    Changes: Database references
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description