1LOC

INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERIAL CELL WALL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction of a legume lectin with two components of the bacterial cell wall. A crystallographic study.

Bourne, Y.Ayouba, A.Rouge, P.Cambillau, C.

(1994) J.Biol.Chem. 269: 9429-9435

  • Primary Citation of Related Structures:  1LOD

  • PubMed Abstract: 
  • We describe herein the refined high resolution x-ray structures of two components of the bacterial cell wall, muramic acid and muramyl dipeptide complexed to isolectin I from Lathyrus ochrus seeds. In both complexes, only the ring hydroxyl oxygen ato ...

    We describe herein the refined high resolution x-ray structures of two components of the bacterial cell wall, muramic acid and muramyl dipeptide complexed to isolectin I from Lathyrus ochrus seeds. In both complexes, only the ring hydroxyl oxygen atoms of the bound sugar establish direct hydrogen bonds with isolectin I, as in the case of all the previously determined monosaccharide-lectin complexes. In addition, the lactyl methyl of both components strongly interacts via hydrophobic contacts with the side chains of residues Tyr100 and Trp128 of isolectin I, which could explain the higher affinity of isolectin I for muramic acid as compared with glucose. These 2 residues, however, are not involved in the stabilization of the oligosaccharide-isolectin I complexes. The dipeptide (D-Ala-D-iGln) of the second component is in stacking interaction with the N-acetyl group of glucose and with loop Gly97-Gly98 of isolectin I. In addition to these van der Waals' contacts, the dipeptide interacts with the lectin via well ordered water molecules also. Superposition of the structures of the muramyl dipeptide complex and of the muramic acid complex shows that the glucose ring in the dipeptide compound is tilted by about 15 degrees in comparison with that of muramic acid. The fact that the lactyl group has the same confrontation in both components reveals that the lectin is stereospecific and recognizes only diastereoisomer S of this group, which better fits the saccharide-binding site.


    Organizational Affiliation

    Laboratorie de Cristallographie et de Cristallisation des Macromolécules Biologiques, Centre National de la Recherche Scientifique Unité de Recherche associée 1296, Faculté de Médecine Secteur-Nord, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (ALPHA CHAIN)
A, C, E, G
181Lathyrus ochrusN/A
Find proteins for P04122 (Lathyrus ochrus)
Go to UniProtKB:  P04122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEGUME ISOLECTIN I (BETA CHAIN)
B, D, F, H
52Lathyrus ochrusN/A
Find proteins for P12306 (Lathyrus ochrus)
Go to UniProtKB:  P12306
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MURAMYL-DIPEPTIDE D-ALA-D-IGLN
1, 2, 3, 4
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DAL
Query on DAL
1, 2, 3, 4
D-PEPTIDE LINKINGC3 H7 N O2

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MDP
Query on MDP
1, 2, 3, 4
D-SACCHARIDEC11 H19 N O9

--

ZGL
Query on ZGL
1, 2, 3, 4
D-peptide linkingC5 H10 N2 O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.580α = 90.00
b = 139.800β = 91.50
c = 63.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance