Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.31 kDa 
• Atom Count: 3654 
• Modelled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

4EW9

The liganded structure of C. bescii family 3 pectate lyase

• PDB DOI: 10.2210/pdb4EW9/pdb

• Classification: LYASE
• Organism(s): Caldicellulosiruptor bescii DSM 6725
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2013-03-20 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction.

Alahuhta, M., Brunecky, R., Chandrayan, P., Kataeva, I., Adams, M.W., Himmel, M.E., Lunin, V.V.

(2013) Acta Crystallogr D Biol Crystallogr 69: 534-539

• PubMed: 23519661 
• DOI: 10.1107/S0907444912050512
• Primary Citation of Related Structures:  
  4EW9


• PubMed Abstract: 
  

The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase catalytic module (PL3-cat) has been structurally described and synergistic digestion studies with C. bescii cellulase A have been performed on unpretreated biomass. The X-ray structure of PL3-cat was determined at 1.6 Å resolution (PDB entry 4ew9) in complex with the products of trigalacturonic acid. Comparison with family 1 pectate lyase (PL1) structures shows that the active site of the PL3 catalytic module is considerably different. However, on superimposing the identical sugar rings at the -2 subsites conserved interactions could be identified. Interestingly, only one catalytic residue, the lysine that donates the proton to the carboxylate group in the β-elimination reaction of PL1 (Lys108 in PL3-cat), is conserved in PL3 and there is no arginine to abstract the proton from the C5 carbon of the galactouronate ring. This suggests that the reaction mechanism of PL3 requires different catalytic residues. Most interestingly, comparison with other proton-abstraction reactions reveals that in PL3 the α-proton is abstracted by a lysine, in a striking similarity to enolases. These observations led us to propose that in PL3-cat Lys108 is the catalytic base, Glu84 is the catalytic acid and an acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Also, our digestion experiments with unpretreated switchgrass show that the loadings of C. bescii cellobiohydrolase A (CelA) can be lowered by the addition of PL3 to the reaction mixture. This result suggests that PL3 can significantly improve the deconstruction of unpretreated biomass by allowing other enzymes to better access their preferred substrates.

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Organizational Affiliation: 

Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401-3305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A, B	195	Caldicellulosiruptor bescii DSM 6725	Mutation(s): 0  Gene Names: Athe_1854 EC: 4.2.2.2
UniProt
Find proteins for B9MKT4 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320)) Explore B9MKT4  Go to UniProtKB:  B9MKT4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G31388FK GlyCosmos:  G31388FK

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADA	N [auth A]	alpha-D-galactopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-BKBMJHBISA-N
DGU	M [auth A], U [auth B]	D-galacturonic acid C6 H10 O7 IAJILQKETJEXLJ-RSJOWCBRSA-N
MPD	J [auth A], K [auth A], L [auth A], T [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	O [auth A], V [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.946	α = 90
b = 35.898	β = 132
c = 98.687	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-26 
• Released Date: 2013-03-20 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 2.0: 2020-07-01
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary