1HV6

CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III COMPLEXED WITH TRISACCHARIDE PRODUCT.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.

Yoon, H.J.Hashimoto, W.Miyake, O.Murata, K.Mikami, B.

(2001) J.Mol.Biol. 307: 9-16

  • DOI: 10.1006/jmbi.2000.4509

  • PubMed Abstract: 
  • The structure of A1-III from a Sphingomonas species A1 complexed with a trisaccharide product (4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was determined by X-ray crystallography at 2.0 A with an R-factor of 0.16. The fin ...

    The structure of A1-III from a Sphingomonas species A1 complexed with a trisaccharide product (4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was determined by X-ray crystallography at 2.0 A with an R-factor of 0.16. The final model of the complex form comprising 351 amino acid residues, 245 water molecules, one sulfate ion and one trisaccharide product exhibited a C(alpha) r.m.s.d. value of 0.154 A with the reported apo form of the enzyme. The trisaccharide was bound in the active cleft at subsites -3 approximately -1 from the non-reducing end by forming several hydrogen bonds and van der Waals interactions with protein atoms. The catalytic residue was estimated to be Tyr246, which existed between subsites -1 and +1 based on a mannuronic acid model oriented at subsite +1.


    Related Citations: 
    • Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A
      Yoon, H.-J.,Mikami, B.,Hashimoto, W.,Murata, K.
      (1999) J.Mol.Biol. 290: 505


    Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALGINATE LYASE
A
351Sphingomonas sp.Gene Names: aly
Find proteins for Q9KWU1 (Sphingomonas sp.)
Go to UniProtKB:  Q9KWU1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GCU
Query on GCU

Download SDF File 
Download CCD File 
A
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-WAXACMCWSA-N
 Ligand Interaction
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
MAV
Query on MAV

Download SDF File 
Download CCD File 
A
alpha-D-mannopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-BYHBOUFCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.765α = 90.00
b = 92.920β = 104.11
c = 82.220γ = 90.00
Software Package:
Software NamePurpose
SADIEdata reduction
SAINTdata reduction
CNSrefinement
SADIE/SAINTdata collection
SAINTdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance