4F10

Alginate lyase A1-III H192A complexed with tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III

Mikami, B.Ban, M.Suzuki, S.Yoon, H.-J.Miyake, O.Yamasaki, M.Ogura, K.Maruyama, Y.Hashimoto, W.Murata, K.

(2012) Acta Crystallogr.,Sect.D 68: 1207-1216

  • DOI: 10.1107/S090744491202495X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] ...

    The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.


    Organizational Affiliation

    Department of Applied Life Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan. mikami@kais.kyoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alginate lyase
A, B
353Sphingomonas spMutation(s): 1 
Gene Names: aly
Find proteins for Q9KWU1 (Sphingomonas sp)
Go to UniProtKB:  Q9KWU1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAW
Query on MAW

Download SDF File 
Download CCD File 
A
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid
C6 H8 O6
IAKKJSVSFCTLRY-NVFHJIOMSA-N
 Ligand Interaction
LGU
Query on LGU

Download SDF File 
Download CCD File 
A, B
ALPHA-L-GULURONATE
alpha-L-gulopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-AZLKCVHYSA-N
 Ligand Interaction
BEM
Query on BEM

Download SDF File 
Download CCD File 
A, B
beta-D-mannuronic acid
(2S,3S,4S,5S,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid
C6 H10 O7
AEMOLEFTQBMNLQ-SYJWYVCOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.386α = 90.00
b = 77.607β = 90.00
c = 145.411γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
FRAMBOdata collection
SAINTdata scaling
PHENIXrefinement
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references