Crystal structure of mutifunctional sialyltransferase from Pasteurella multocida with CMP bound

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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Cytidine 5'-Monophosphate (CMP)-Induced Structural Changes in a Multifunctional Sialyltransferase from Pasteurella multocida

Ni, L.Sun, M.Yu, H.Chokhawala, H.Chen, X.Fisher, A.J.

(2006) Biochemistry 45: 2139-2148

  • DOI: https://doi.org/10.1021/bi0524013
  • Primary Citation of Related Structures:  
    2EX0, 2EX1

  • PubMed Abstract: 

    Sialyltransferases catalyze reactions that transfer a sialic acid from CMP-sialic acid to an acceptor (a structure terminated with galactose, N-acetylgalactosamine, or sialic acid). They are key enzymes that catalyze the synthesis of sialic acid-containing oligosaccharides, polysaccharides, and glycoconjugates that play pivotal roles in many critical physiological and pathological processes. The structures of a truncated multifunctional Pasteurella multocida sialyltransferase (Delta24PmST1), in the absence and presence of CMP, have been determined by X-ray crystallography at 1.65 and 2.0 A resolutions, respectively. The Delta24PmST1 exists as a monomer in solution and in crystals. Different from the reported crystal structure of a bifunctional sialyltransferase CstII that has only one Rossmann domain, the overall structure of the Delta24PmST1 consists of two separate Rossmann nucleotide-binding domains. The Delta24PmST1 structure, thus, represents the first sialyltransferase structure that belongs to the glycosyltransferase-B (GT-B) structural group. Unlike all other known GT-B structures, however, there is no C-terminal extension that interacts with the N-terminal domain in the Delta24PmST1 structure. The CMP binding site is located in the deep cleft between the two Rossmann domains. Nevertheless, the CMP only forms interactions with residues in the C-terminal domain. The binding of CMP to the protein causes a large closure movement of the N-terminal Rossmann domain toward the C-terminal nucleotide-binding domain. Ser 143 of the N-terminal domain moves up to hydrogen-bond to Tyr 388 of the C-terminal domain. Both Ser 143 and Tyr 388 form hydrogen bonds to a water molecule, which in turn hydrogen-bonds to the terminal phosphate oxygen of CMP. These interactions may trigger the closure between the two domains. Additionally, a short helix near the active site seen in the apo structure becomes disordered upon binding to CMP. This helix may swing down upon binding to donor CMP-sialic acid to form the binding pocket for an acceptor.

  • Organizational Affiliation

    Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
a2,3-sialyltransferase, a2,a6-sialyltransferase399Pasteurella multocidaMutation(s): 0 
Gene Names: Pm0188
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for Q15KI8 (Pasteurella multocida)
Explore Q15KI8 
Go to UniProtKB:  Q15KI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15KI8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C5P

Download Ideal Coordinates CCD File 
C9 H14 N3 O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.255α = 90
b = 64.571β = 98.62
c = 64.84γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description