6HTV

Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with isomaltotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Futile Encounter Engineering of the DSR-M Dextransucrase Modifies the Resulting Polymer Length.

Claverie, M.Cioci, G.Guionnet, M.Schorghuber, J.Lichtenecker, R.Moulis, C.Remaud-Simeon, M.Lippens, G.

(2019) Biochemistry 58: 2853-2859

  • DOI: 10.1021/acs.biochem.9b00373
  • Primary Citation of Related Structures:  
    6HTV

  • PubMed Abstract: 
  • The factors that define the resulting polymer length of distributive polymerases are poorly understood. Here, starting from the crystal structure of the dextransucrase DSR-M in complex with an isomaltotetraose, we define different anchoring points for the incoming acceptor ...

    The factors that define the resulting polymer length of distributive polymerases are poorly understood. Here, starting from the crystal structure of the dextransucrase DSR-M in complex with an isomaltotetraose, we define different anchoring points for the incoming acceptor. Mutation of one of these, Trp624, decreases the catalytic rate of the enzyme but equally skews the size distribution of the resulting dextran chains toward shorter chains. Nuclear magnetic resonance analysis shows that this mutation influences both the dynamics of the active site and the water accessibility. Monte Carlo simulation of the elongation process allows interpretation of these results in terms of enhanced futile encounters, whereby the less effective binding increases the pool of effective seeds for the dextran chains and thereby directly determines the length distribution of the final polymers.


    Organizational Affiliation

    LISBP , Université de Toulouse, CNRS, INRA, INSA , 31400 Toulouse , France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AlternansucraseA1,290Leuconostoc citreumMutation(s): 0 
Gene Names: asr
EC: 2.4.1.140 (PDB Primary Data), 2.4.1.5 (UniProt)
UniProt
Find proteins for A0A2H4A2Q1 (Leuconostoc citreum)
Explore A0A2H4A2Q1 
Go to UniProtKB:  A0A2H4A2Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4A2Q1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranoseB 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80662SX
GlyCosmos:  G80662SX
GlyGen:  G80662SX
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.308α = 90
b = 185.308β = 90
c = 150.774γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary