Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.01 kDa 
• Atom Count: 2,773 
• Modelled Residue Count: 324 
• Deposited Residue Count: 326 
• Unique protein chains: 1

 3VMW

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

• PDB DOI: 10.2210/pdb3VMW/pdb

• Classification: LYASE
• Organism(s): Bacillus sp. N16-5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-17 Released: 2012-07-25 
• Deposition Author(s): Zheng, Y., Huang, C.H., Liu, W., Ko, T.P., Xue, Y., Zhou, C., Zhang, G., Guo, R.T., Ma, Y.

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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 

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

• PubMed: 22414692 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A	326	Bacillus sp. N16-5	Mutation(s): 0  Gene Names: GU088530, pelA EC: 4.2.2.2
UniProt
Find proteins for D0VP31 (Bacillus sp. N16-5) Explore D0VP31  Go to UniProtKB:  D0VP31

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid	B	3		N/A
Glycosylation Resources
GlyTouCan:  G29175YU GlyCosmos:  G29175YU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 137.902	α = 90
b = 48.174	β = 90
c = 52.47	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Zheng, Y., Huang, C.H., Liu, W., Ko, T.P., Xue, Y., Zhou, C., Zhang, G., Guo, R.T., Ma, Y.

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