1E9L

The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

The Crystal Structure of a Novel Mammalian Lectin, Ym1, Suggests a Saccharide Binding Site

Sun, Y.J.Chang, N.C.Hung, S.I.Chang, A.C.Chou, C.C.Hsiao, C.D.

(2001) J Biol Chem 276: 17507

  • DOI: 10.1074/jbc.M010416200
  • Primary Citation of Related Structures:  
    1E9L

  • PubMed Abstract: 
  • Ym1, a secretory protein synthesized by activated murine peritoneal macrophages, is a novel mammalian lectin with a binding specificity to GlcN. Lectins are responsible for carbohydrate recognition and for mediating cell-cell and cell-extracellular m ...

    Ym1, a secretory protein synthesized by activated murine peritoneal macrophages, is a novel mammalian lectin with a binding specificity to GlcN. Lectins are responsible for carbohydrate recognition and for mediating cell-cell and cell-extracellular matrix interactions in microbes, plants, and animals. Glycosaminoglycan heparin/heparan sulfate binding ability was also detected in Ym1. We report here the three-dimensional structure of Ym1 at 2.5-A resolution by x-ray crystallography. The crystal structure of Ym1 consists of two globular domains, a beta/alpha triose-phosphate isomerase barrel domain and a small alpha + beta folding domain. A notable electron density of sugar is detected in the Ym1 crystal structure. The saccharide is located inside the triose-phosphate isomerase domain at the COOH terminal end of the beta-strands. Both hydrophilic and hydrophobic interactions are noted in the sugar-binding site in Ym1. Despite the fact that Ym1 is not a chitinase, structurally, Ym1 shares significant homology with chitinase A of Serratia marcescens. Ym1 and chitinase A have a similar carbohydrate binding cleft. This study provides new structure information, which will lead to better understanding of the biological significance of Ym1 and its putative gene members.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YM1 SECRETORY PROTEINA377Mus musculusMutation(s): 0 
Gene Names: Chil3Chi3l3Ym1
EC: 3.2.1.52
Find proteins for O35744 (Mus musculus)
Explore O35744 
Go to UniProtKB:  O35744
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCS
Query on GCS

Download CCD File 
A
2-amino-2-deoxy-beta-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 60.66β = 94.61
c = 60.76γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2000-10-21 
  • Released Date: 2001-03-01 
  • Deposition Author(s): Hsiao, C.D., Sun, Y.J.

Revision History 

  • Version 1.0: 2001-03-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-05-22
    Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description
  • Version 2.1: 2020-07-01
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary