5XNR

Truncated AlyQ with CBM32 and alginate lyase domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2.

Sim, P.F.Furusawa, G.Teh, A.H.

(2017) Sci Rep 7: 13656-13656

  • DOI: 10.1038/s41598-017-13288-1

  • PubMed Abstract: 
  • AlyQ from Persicobacter sp. CCB-QB2 is an alginate lyase with three domains - a carbohydrate-binding domain modestly resembling family 16 carbohydrate-binding module (CBM16), a family 32 CBM (CBM32) domain, and an alginate lyase domain belonging to p ...

    AlyQ from Persicobacter sp. CCB-QB2 is an alginate lyase with three domains - a carbohydrate-binding domain modestly resembling family 16 carbohydrate-binding module (CBM16), a family 32 CBM (CBM32) domain, and an alginate lyase domain belonging to polysaccharide lyase family 7 (PL7). Although AlyQ can also act on polyguluronate (poly-G) and polymannuronate (poly-M), it is most active on alginate. Studies with truncated AlyQ showed that the CBM32 domain did not contribute to enhancing AlyQ's activity under the assayed conditions. Nevertheless, it could bind to cleaved but not intact alginate, indicating that the CBM32 domain recognises alginate termini. The crystal structure containing both CBM32 and catalytic domains show that they do not interact with one another. The CBM32 domain contains a conserved Arg that may bind to the carboxyl group of alginate. The catalytic domain, meanwhile, shares a conserved substrate-binding groove, and the presence of two negatively charged Asp residues may dictate substrate specificity especially at subsite +1. As Persicobacter sp. CCB-QB2 was unable to utilise alginate, AlyQ may function to help the bacterium degrade cell walls more efficiently.


    Organizational Affiliation

    Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Bayan Lepas, Penang, Malaysia.,Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Bayan Lepas, Penang, Malaysia. aikhong@usm.my.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlyQ
A
398Persicobacter sp. CCB-QB2Mutation(s): 0 
Find proteins for A0A3B6UEP6 (Persicobacter sp. CCB-QB2)
Go to UniProtKB:  A0A3B6UEP6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.317α = 90.00
b = 74.317β = 90.00
c = 179.733γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-24 
  • Released Date: 2018-06-13 
  • Deposition Author(s): Teh, A.H., Sim, P.F.

Funding OrganizationLocationGrant Number
Malaysia--

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release