PDBsum entry: 1hv6

Lyase

PDB-id: 1hv6

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

351 a.a. *

Ligands

MAW-MAV-GCU

SO4

Waters ×245

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1hv6

Name:

Lyase

Title:

Crystal structure of alginate lyase a1-iii complexed with trisaccharide product.

Structure:

Alginate lyase. Chain: a. Fragment: residue 52-402. Engineered: yes

Source:

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

Biological unit:

Dimer (from PQS)

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:

2.00Å

R-factor:

0.158

R-free:

0.197

Authors:

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

Key ref:

H.J.Yoon et al. (2001). Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.. J Mol Biol, 307, 9. [PubMed id: 11243798] [DOI: 10.1006/jmbi.2000.4509]

Date:

08-Jan-01

Release date:

02-May-01

Related entries:

1qaz
1qza contains the same protein in apo form.

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.2000.4509

J Mol Biol 307:9 (2001)

PubMed id: 11243798

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

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

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 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.

Selected figure(s)

Figure 3.
Figure 3. (a) The bound trisaccharide molecule on the active site of A1-III. The Figure shows the bound trisaccharide molecule and the surrounding amino acid residues and water molecules interacting with the trisaccharide. The trisaccharide molecule is represented by means of an orange ball-and-stick model. The side-chains of Tyr and Trp, Asn and Gln, Asp, Arg, and His residues are colored yellow, green, red, cyan and purple, respectively. The water molecules are shown as a filled circle ( o ). The hydrogen bonds between trisaccharide and protein residues or water molecules less than 3.25 Å are shown as dotted lines. This Figure was drawn using the program GRASP.[23] (b) The conformational change of A1-III induced by the binding of trisaccharide products. A1-III and A1-III with trisaccharide structures are represented as thin and thick lines, respectively. The water molecules are shown as a filled circle ( o ). The hydrogen bonds in trisaccharide, protein residues or water molecules less than 3.25 Å are shown as dotted lines. This Figure was prepared using the programs TURBO-FRODO (Bio-Graphics) on a Silicon Graphics INDY computer and Adobe Illustrator 5.5.

Figure 4.
Figure 4. (a) Stereo diagram showing the spatial orientation of M - 1, reducing end of the bound trisaccharide product with manually constructed M+1 in the catalytic site of A1-III. (b) Schematic representation of polymannuronic acid degradation mechanism. (1) Arg239 interacts with the carboxyl group of M+1 and with Tyr246 to stabilize the negative charge of the ionized side-chain. His192 is hydrogen-bonded to O-5 of the sugar. Tyr246 is positioned close to O-4 and C-5. (2) Tyr246 extracts the proton of C-5, resulting in the formation of a carboxylate dianion intermediate. (3) Tyr246 donates a proton to the glycosidic oxygen, resulting in the cleavage of the glycosidic bond and the formation of a double bond between the C-4 and C-5 atoms.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 9-0) copyright 2001.

Figures were selected by an automated process.