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

PDB DOI: 10.2210/pdb7DFO/pdb

Classification: HYDROLASE
Organism(s): Streptomyces olivaceoviridis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-09 Released: 2020-12-30
Deposition Author(s): Fujimoto, Z., Kishine, N., Kaneko, S.

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 1.2 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

PubMed: 33564921 Search on PubMed
DOI: 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 ³Xyl 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 ³Xyl 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:

Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan. sakaneko@agr.u-ryukyu.ac.jp.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A, B, C, D, E, F, G, H, I A, B, C, D, E, F, G, H, I	205	Streptomyces olivaceoviridis	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7G1MBT0
Protein Feature View Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	J, M, O, P	3		N/A	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G87429QT GlyCosmos: G87429QT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D 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	5		N/A	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G20006DY GlyCosmos: G20006DY

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	L	4		N/A	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G75464GU GlyCosmos: G75464GU

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	Q	2		N/A	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G87728WL GlyCosmos: G87728WL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain DB [auth H] SDF format, chain EA [auth C] SDF format, chain EB [auth H] SDF format, chain FA [auth C] SDF format, chain FB [auth H] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain HB [auth I] SDF format, chain IA [auth D] SDF format, chain IB [auth I] SDF format, chain JA [auth D] SDF format, chain JB [auth I] SDF format, chain KB [auth I] SDF format, chain LB [auth I] SDF format, chain MB [auth I] SDF format, chain NB [auth I] SDF format, chain OA [auth D] SDF format, chain OB [auth I] SDF format, chain PA [auth D] SDF format, chain PB [auth I] SDF format, chain QA [auth E] SDF format, chain QB [auth I] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain T [auth A] SDF format, chain TA [auth E] SDF format, chain U [auth A] SDF format, chain UA [auth E] SDF format, chain V [auth A] SDF format, chain WA [auth F] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth B] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth I] MOL2 format, chain KB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain MB [auth I] MOL2 format, chain NB [auth I] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth I] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth I] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth I] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth G]	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		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain RB [auth I] SDF format, chain SB [auth I] SDF format, chain TB [auth I] SDF format, chain UB [auth I] SDF format, chain VA [auth E] SDF format, chain W [auth A] SDF format, chain YA [auth F] SDF format, chain Z [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain RB [auth I] MOL2 format, chain SB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain UB [auth I] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B]	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		Ligand Interaction