PDBsum entry: 1qaz

Lyase

PDB-id: 1qaz

Biological unit = asymmetric unit,
as shown
(as defined in PDB file)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

351 a.a. *

Ligands

SO4 ×2

Waters ×298

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1qaz

Name:

Lyase

Title:

Crystal structure of alginate lyase a1-iii from sphingomonas species a1 at 1.78a resolution

Structure:

Protein (alginate lyase a1-iii). Chain: a. Engineered: yes

Source:

Sphingomonas sp.. Organism_taxid: 28214. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.

Biological unit:

Monomer (from PDB file)

UniProt:

Q9KWU1 (Q9KWU1_9SPHN)

Seq:

Struc:

Seq:

Struc:

Seq:

641 a.a.

Struc:

351 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Resolution:

1.78Å

R-factor:

0.180

R-free:

0.233

Authors:

H.-J.Yoon

Key ref:

H.J.Yoon et al. (1999). Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.. J Mol Biol, 290, 505-514. [PubMed id: 10390348] [DOI: 10.1006/jmbi.1999.2883]

Date:

08-Apr-99

Release date:

19-Jul-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.1999.2883

J Mol Biol 290:505-514 (1999)

PubMed id: 10390348

Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.

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

ABSTRACT

The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.

Selected figure(s)

Figure 3.
Figure 3. Overall structure of the ALYIII ribbon stereo-diagram. The Figure shows loops (red), 12 a-helices (blue), two sulfate ions (green), and two S-S bridges, Cys49 - Cys112 and Cys188 - Cys189 (yel- low). The 12 a-helices are num- bered from the N-terminal. The bound sulfate ions and the cystine residues are represented as ball- and-sticks. The Figure was pre- pared using the programs MOL- SCRIPT (Kraulis, 1991) and RASTER3D (Merrit & Murphy, 1994).

Figure 10.
Figure 10. Structural comparison of a-helices within the a/a-barrel structure of ALYIII (blue), gluco- amylase (yellow) and cellulase (pink). The superimposed result is shown as a schematic view in C a -traces of a-helices. The co- ordinates of glucoamylase (1DOG) and cellulase (1CEM) were taken from the Brookhaven Protein Data Bank.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 290, 505-514) copyright 1999.

Figures were selected by an automated process.