4YZ0

C. bescii Family 3 pectate lyase double mutant K108A/E39Q in complex with trigalacturonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.

Alahuhta, M.Taylor, L.E.Brunecky, R.Sammond, D.W.Michener, W.Adams, M.W.Himmel, M.E.Bomble, Y.J.Lunin, V.

(2015) Acta Crystallogr.,Sect.D 71: 1946-1954

  • DOI: 10.1107/S1399004715013760
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures ...

    The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment.


    Organizational Affiliation

    BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pectate lyase
A, B
204Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320)Mutation(s): 2 
EC: 4.2.2.2
Find proteins for B9MKT4 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320))
Go to UniProtKB:  B9MKT4
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTR
Query on GTR

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Download CCD File 
A, B
Beta-D-Galactopyranuronic acid
Galacturonic acid
C6 H10 O7
AEMOLEFTQBMNLQ-DTEWXJGMSA-N
 Ligand Interaction
X1X
Query on X1X

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Download CCD File 
A
alpha-D-talopyranuronic acid
alpha-D-taluronate
C6 H10 O7
AEMOLEFTQBMNLQ-JWKHNPINSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
X0X
Query on X0X

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Download CCD File 
B
beta-D-talopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-BYVYFCENSA-N
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ADA
Query on ADA

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A, B
ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.116 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 138.290α = 90.00
b = 36.470β = 132.63
c = 100.070γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United States--

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations