7DFO

Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl xylotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.

Fujimoto, Z.Kishine, N.Teramoto, K.Tsutsui, S.Kaneko, S.

(2021) Appl Microbiol Biotechnol 105: 1943-1952

  • DOI: https://doi.org/10.1007/s00253-021-11098-0
  • Primary Citation of Related Structures:  
    7DFM, 7DFN, 7DFO

  • PubMed Abstract: 

    Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the - side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite - 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-β-D-xylopyranosyl-(1→4)-[O-α-L-arabinofuranosyl-(1→3)]-O-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (Ara 3 Xyl 4 ) and O-β-D-xylopyranosyl-(1→4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(l→2)]-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (MeGlcA 3 Xyl 4 ) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a β-jerryroll fold structure, and the catalytic cleft is located on the inner β-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and - 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides. KEY POINTS: • Crystal structure of family 11 β-xylanase from Streptomyces olivaceoviridis was determined. • Topology of substrate-binding cleft of family 11 β-xylanase from Streptomyces olivaceoviridis was characterized. • Mode of action of family 11 β-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated.


  • Organizational Affiliation

    Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, 305-8518, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase
A, B, C, D, E
A, B, C, D, E, F, G, H, I
205Streptomyces olivaceoviridisMutation(s): 0 
Gene Names: soxB
EC: 3.2.1.8
UniProt
Find proteins for A0A7G1MBT0 (Streptomyces olivaceoviridis)
Explore A0A7G1MBT0 
Go to UniProtKB:  A0A7G1MBT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7G1MBT0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
J, M, O, P
3N/A
Glycosylation Resources
GlyTouCan:  G87429QT
GlyCosmos:  G87429QT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
K, N
5N/A
Glycosylation Resources
GlyTouCan:  G20006DY
GlyCosmos:  G20006DY
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
L
4N/A
Glycosylation Resources
GlyTouCan:  G75464GU
GlyCosmos:  G75464GU
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
Q
2N/A
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth G]
BA [auth C]
BB [auth G]
CA [auth C]
AA [auth C],
AB [auth G],
BA [auth C],
BB [auth G],
CA [auth C],
CB [auth G],
DA [auth C],
DB [auth H],
EA [auth C],
EB [auth H],
FA [auth C],
FB [auth H],
GB [auth H],
HA [auth D],
HB [auth I],
IA [auth D],
IB [auth I],
JA [auth D],
JB [auth I],
KB [auth I],
LB [auth I],
MB [auth I],
NB [auth I],
OA [auth D],
OB [auth I],
PA [auth D],
PB [auth I],
QA [auth E],
QB [auth I],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
T [auth A],
TA [auth E],
U [auth A],
UA [auth E],
V [auth A],
WA [auth F],
X [auth B],
XA [auth F],
Y [auth B],
ZA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth C]
KA [auth D]
LA [auth D]
MA [auth D]
NA [auth D]
GA [auth C],
KA [auth D],
LA [auth D],
MA [auth D],
NA [auth D],
RB [auth I],
SB [auth I],
TB [auth I],
UB [auth I],
VA [auth E],
W [auth A],
YA [auth F],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.709α = 90
b = 142.709β = 90
c = 72.454γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description