6HF4

The structure of BoMan26B, a GH26 beta-mannanase from Bacteroides ovatus, complexed with G1M4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A surface-exposed GH26 beta-mannanase fromBacteroides ovatus: Structure, role, and phylogenetic analysis ofBoMan26B.

Bagenholm, V.Wiemann, M.Reddy, S.K.Bhattacharya, A.Rosengren, A.Logan, D.T.Stalbrand, H.

(2019) J Biol Chem 294: 9100-9117

  • DOI: 10.1074/jbc.RA118.007171
  • Primary Citation of Related Structures:  
    6HF2, 6HF4

  • PubMed Abstract: 
  • The galactomannan utilization locus ( Bo ManPUL) of the human gut bacterium Bacteroides ovatus encodes Bo Man26B, a cell-surface-exposed endomannanase whose functional and structural features have been unclear. Our study now places Bo Man26B in context with related enzymes and reveals the structural basis for its specificity ...

    The galactomannan utilization locus ( Bo ManPUL) of the human gut bacterium Bacteroides ovatus encodes Bo Man26B, a cell-surface-exposed endomannanase whose functional and structural features have been unclear. Our study now places Bo Man26B in context with related enzymes and reveals the structural basis for its specificity. Bo Man26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase Bo Man26A of the same locus. Using galactomannan, Bo Man26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface-exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of Bo Man26B and the periplasmic α-galactosidase Bo Gal36A increased the rate of galactose release by about 10-fold compared with the rate without Bo Man26B. The results suggested that Bo Man26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by Bo Gal36A. A crystal structure of Bo Man26B with galactosyl-mannotetraose bound in subsites -5 to -2 revealed an open and long active-site cleft with Trp-112 in subsite -5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the -4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that Bo Man26A and Bo Man26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B.


    Organizational Affiliation

    From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and henrik.stalbrand@biochemistry.lu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 26A368Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_02093
UniProt
Find proteins for A7LW89 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153))
Explore A7LW89 
Go to UniProtKB:  A7LW89
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranoseB5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80515RB
GlyCosmos:  G80515RB
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.122α = 90
b = 68.363β = 90
c = 94.993γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden213-2014-1254

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary