4AYP

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside

• PDB DOI: https://doi.org/10.2210/pdb4AYP/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter sp. K31
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-21 Released: 2013-01-30 
• Deposition Author(s): Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Iglesias-Fernandez, A., Dinev, Z., Williams, S.J., Siriwardena, A., Moreland, C., Hu, T.C., Smith, D.K., Gilbert, H.J., Rovira, C., Davies, G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 0.106 
• R-Value Work: 0.096 
• R-Value Observed: 0.097 

Starting Model: experimental

Literature

The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.

Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Ardevol, A., Dinev, Z., Williams, S.J., Bande, O., Siriwardena, A., Moreland, C., Hu, T.C., Smith, D.K., Gilbert, H.J., Rovira, C., Davies, G.J.

(2012) Angew Chem Int Ed Engl 51: 10997

• PubMed: 23012075 
• DOI: https://doi.org/10.1002/anie.201205338
• Primary Citation of Related Structures:  
  4AYO, 4AYP, 4AYQ, 4AYR


• PubMed Abstract: 
  

  Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an inverting α-mannosidase show how the enzyme distorts the substrate and transition state. QM/MM calculations reveal how the free energy landscape of isolated α-D-mannose is molded on enzyme to only allow one conformationally accessible reaction coordinate.

---

Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.02 kDa 
• Atom Count: 4,452 
• Modelled Residue Count: 434 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE	A	447	Caulobacter sp. K31	Mutation(s): 0  EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31)) Explore B0SWV2  Go to UniProtKB:  B0SWV2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside	B	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G32183TR GlyCosmos:  G32183TR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900033	B	methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 0.106 
• R-Value Work: 0.096 
• R-Value Observed: 0.097 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.135	α = 90
b = 144.135	β = 90
c = 50.301	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Iglesias-Fernandez, A., Dinev, Z., Williams, S.J., Siriwardena, A., Moreland, C., Hu, T.C., Smith, D.K., Gilbert, H.J., Rovira, C., Davies, G.J.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description, Structure summary