PDBsum entry 1gxo

Lyase

PDB id: 1gxo

Contents

Protein chain

320 a.a. *

Ligands

ADA-ADA-ADA

Metals

_CA

Waters ×171

* Residue conservation analysis

PDB id:

1gxo

Name:

Lyase

Title:

Mutant d189a of family 10 polysaccharide lyase from cellvibrio cellulosa in complex with trigalaturonic acid

Structure:

Pectate lyase. Chain: a. Fragment: catalytic module, residues 327-649. Synonym: polygalacturonic acid lyase. Engineered: yes. Mutation: yes. Other_details: complex with trigalacturonic acid

Source:

Cellvibrio cellulosa. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3.

Resolution:

2.05Å R-factor: 0.176 R-free: 0.228

Authors:

S.J.Charnock,I.E.Brown,J.P.Turkenburg,G.W.Black,G.J.Davies

Key ref:

S.J.Charnock et al. (2002). Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci U S A, 99, 12067-12072. PubMed id: 12221284 DOI: 10.1073/pnas.182431199

Date:

08-Apr-02 Release date: 04-Oct-02

Protein chain

Q9F7L3  (Q9F7L3_CELJA) -  Pectate lyase from Cellvibrio japonicus

Seq: 649 a.a.

Struc: 320 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.4.2.2.2 - pectate lyase.
• Pathway: Pectin and Pectate Lyases
• Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.

DOI no: 10.1073/pnas.182431199

Proc Natl Acad Sci U S A 99:12067-12072 (2002)

PubMed id: 12221284

Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.

S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, G.J.Davies.

ABSTRACT

Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the -1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.

Selected figure(s)

Figure 3.
Fig 3. Schematic diagram of the interactions of the mutant D389A Pel10Acm with trigalacturonate. The approximate location of Asp389 from the native structure is indicated for reference.

Figure 4.
Fig 4. (a) More O'Ferral diagram for -elimination of galacto-configured uronic acids. (b) Putative E1cb/asynchronous E2 reaction mechanism for Pel10 and related enzymes in which proton abstraction by arginine is followed by leaving-group elimination. The essential role of Asp389 may involve a role in binding a second Ca^2+ ion as observed in Pel1C.

Figures were selected by an automated process.