4WQQ

Structure of EPNH mutant of CEL-I

• PDB DOI: https://doi.org/10.2210/pdb4WQQ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cucumaria echinata
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-22 Released: 2015-04-29 
• Deposition Author(s): Unno, H., Hatakeyama, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Mannose-recognition mutant of the galactose/N-acetylgalactosamine-specific C-type lectin CEL-I engineered by site-directed mutagenesis.

Moriuchi, H., Unno, H., Goda, S., Tateno, H., Hirabayashi, J., Hatakeyama, T.

(2015) Biochim Biophys Acta 1850: 1457-1465

• PubMed: 25869490 
• DOI: https://doi.org/10.1016/j.bbagen.2015.04.004
• Primary Citation of Related Structures:  
  4WQQ


• PubMed Abstract: 
  

  CEL-I is a galactose/N-acetylgalactosamine-specific C-type lectin isolated from the sea cucumber Cucumaria echinata. Its carbohydrate-binding site contains a QPD (Gln-Pro-Asp) motif, which is generally recognized as the galactose specificity-determining motif in the C-type lectins. In our previous study, replacement of the QPD motif by an EPN (Glu-Pro-Asn) motif led to a weak binding affinity for mannose. Therefore, we examined the effects of an additional mutation in the carbohydrate-binding site on the specificity of the lectin.

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Organizational Affiliation: 

Laboratory of Biomolecular Chemistry, Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.72 kDa 
• Atom Count: 5,385 
• Modelled Residue Count: 564 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type	A, B, C, D	141	Cucumaria echinata	Mutation(s): 3
UniProt
Find proteins for Q7M462 (Cucumaria echinata) Explore Q7M462  Go to UniProtKB:  Q7M462

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	H [auth A], L [auth B], P [auth C], T [auth D]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MAN	Binding MOAD:  4WQQ	Ka: 3170 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.29	α = 90
b = 61.06	β = 109.39
c = 80.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Unno, H., Hatakeyama, T.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary