3VMW

Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165 in complex with trigalacturonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5.

Zheng, Y.Huang, C.H.Liu, W.Ko, T.P.Xue, Y.Zhou, C.Guo, R.T.Ma, Y.

(2012) Biochem Biophys Res Commun 420: 269-274

  • DOI: 10.1016/j.bbrc.2012.02.148
  • Primary Citation of Related Structures:  
    3VMV, 3VMW

  • PubMed Abstract: 
  • The pectate lyase (Bsp165PelA) from Bacillus sp. N16-5 has great potential in industrial applications because it shows high specific activity under extremely alkaline conditions. Besides, activity measurement of Bsp165PelA does not require addition o ...

    The pectate lyase (Bsp165PelA) from Bacillus sp. N16-5 has great potential in industrial applications because it shows high specific activity under extremely alkaline conditions. Besides, activity measurement of Bsp165PelA does not require addition of calcium, in a way different from the other pectate lyases. Here we report crystal structures of Bsp165PelA in apo-form and in complex with trigalacturonate. The parallel β-helix, active site residues and substrate binding cleft are similar to those in the other pectate lyases from Polysaccharide Lyase family 1. However, some of the highly conserved Ca(2+) binding residues and secondary structures are altered in Bsp165PelA, making it difficult to coordinate with Ca(2+) as in the other pectate lyases. We found Bsp165PelA forms some direct enzyme-substrate interactions instead of using Ca(2+) ions bridging in the extremely alkaline environment.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pectate lyaseA326Bacillus sp. N16-5Mutation(s): 0 
Gene Names: GU088530pelA
EC: 4.2.2.2
Find proteins for D0VP31 (Bacillus sp. N16-5)
Explore D0VP31 
Go to UniProtKB:  D0VP31
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid
B
3 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.902α = 90
b = 48.174β = 90
c = 52.47γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary