8Y1M

Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.

Nakamura, T.Takita, T.Kuwata, K.Mizutani, K.Mikami, B.Nakamura, S.Yasukawa, K.

(2024) Sci Rep 14: 7767-7767

  • DOI: https://doi.org/10.1038/s41598-024-57819-z
  • Primary Citation of Related Structures:  
    8XY0, 8Y1M

  • PubMed Abstract: 

    XynR is a thermostable alkaline GH10 xylanase, for which we have previously examined the effects of saturation mutagenesis at position 315 on enzyme alkaliphily, and found that at pH 10, the activities of variants could be ordered as follows: T315Q > T315S = T315N > T315H = wild-type XynR (WT) > 15 other variants. In this study, we sought to elucidate the mechanisms underlying the variable activity of these different variants. Crystallographic analysis revealed that the Ca 2+ ion near position 315 in WT was absent in the T315Q variant. We accordingly hypothesized that the enhancement of alkaliphily in T315Q, and probably also in the T315H, T315N, and T315S variants, could be ascribed to an activity-stability trade-off associated with a reduction in stability due to the lack of this Ca 2+ ion. Consistent with expectations, the alkaline resistance of T315H, T315N, T315Q, and T315S, evaluated through the pH-dependence of stability at 0 mM CaCl 2 under alkaline conditions, was found to be lower than that of WT: the residual activity at pH 11 of WT was 78% while those of T315H, T315N, T315Q, and T315S were 0, 9, 0, and 43%, respectively. In addition, the thermostabilities of these four variants, as assessed using the denaturing temperatures (T m ) at 0 mM CaCl 2 based on ellipticity at 222 nm in circular dichroism measurements, were lower than that of WT by 2-8 °C. Furthermore, the T m values of WT and variants at 5 mM CaCl 2 were higher than those at 0 mM CaCl 2 by 6-11 °C. Collectively, our findings in this study indicate that mutation of the T residue at position 315 of XynR to H, N, Q, and S causes an increase in the alkaliphily of this enzyme, thereby reducing its stability.


  • Organizational Affiliation

    Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase A
A, B
360Bacillus sp. TAR1Mutation(s): 0 
Gene Names: xynABH2120
EC: 3.2.1.8
UniProt
Find proteins for P07528 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore P07528 
Go to UniProtKB:  P07528
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07528
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
C, D, E, F
2N/A
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
DA [auth B],
S [auth A],
T [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
N [auth A]
O [auth A]
P [auth A]
BA [auth B],
CA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth B],
U [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth B],
L [auth A],
M [auth A],
Z [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.702α = 90
b = 53.335β = 93.58
c = 96.567γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan30397559

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release