Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 117 kDa 
• Atom Count: 8,747 
• Modelled Residue Count: 1,040 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

 6F2P

Structure of Paenibacillus xanthan lyase to 2.6 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb6F2P/pdb

• Classification: LYASE
• Organism(s): Paenibacillus
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2017-11-27 Released: 2018-12-05 
• Deposition Author(s): Lo Leggio, L., Kadziola, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity.

Jensen, P.F., Kadziola, A., Comamala, G., Segura, D.R., Anderson, L., Poulsen, J.N., Rasmussen, K.K., Agarwal, S., Sainathan, R.K., Monrad, R.N., Svendsen, A., Nielsen, J.E., Lo Leggio, L., Rand, K.D.

(2019) Cell Chem Biol 26: 191-202.e6

• PubMed: 30503284 
• DOI: https://doi.org/10.1016/j.chembiol.2018.10.016
• Primary Citation of Related Structures:  
  6F2P


• PubMed Abstract: 
  

We have characterized the structure and dynamics of the carbohydrate-modifying enzyme Paenibacillus nanensis xanthan lyase (PXL) involved in the degradation of xanthan by X-ray crystallography, small-angle X-ray scattering, and hydrogen/deuterium exchange mass spectrometry. Unlike other xanthan lyases, PXL is specific for both unmodified mannose and pyruvylated mannose, which we find is correlated with structural differences in the substrate binding groove. The structure of the full-length enzyme reveals two additional C-terminal modules, one of which belongs to a new non-catalytic carbohydrate binding module family. Ca ²⁺ are critical for the activity and conformation of PXL, and we show that their removal by chelating agents results in localized destabilization/unfolding of particularly the C-terminal modules. We use the structure and the revealed impact of Ca ²⁺ coordination on conformational dynamics to guide the engineering of PXL variants with increased activity and stability in a chelating environment, thus expanding the possibilities for industrial applications of PXL.

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Organizational Affiliation: 

Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Paenibacillus xanthan lyase	A	1,040	Paenibacillus	Mutation(s): 0  EC: 4.2.2.12
UniProt
Find proteins for A0A493R6T1 (Paenibacillus) Explore A0A493R6T1  Go to UniProtKB:  A0A493R6T1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	O [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
MPD	BA [auth A], DA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], W [auth A], Y [auth A], Z [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	AA [auth A], CA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.61	α = 90
b = 100.61	β = 90
c = 324.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Lo Leggio, L., Kadziola, A.

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Database references