PDBsum entry: 1gxm

Lyase

PDB-id: 1gxm

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PROCHECK

Protein chains

324 a.a. *

Ligands

GOL ×4

Waters ×835

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1gxm

Name:

Lyase

Title:

Family 10 polysaccharide lyase from cellvibrio cellulosa

Structure:

Pectate lyase. Chain: a, b. Fragment: catalytic module, residues 327-649. Synonym: polygalacturonic acid lyase. Engineered: yes

Source:

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

UniProt:

Chains A, B: Q9F7L3 (Q9F7L3_9GAMM)

Seq:

Struc:

Seq:

Struc:

Seq:

649 a.a.

Struc:

324 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

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

Resolution:

1.32Å

R-factor:

0.132

R-free:

0.162

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

Related entries:

1gxn family 10 polysaccharide lyase from pseudemonas cellulosa
1gxo mutant d189a of family 10 polysaccharide lyase from pseudemonas cellulosa in complex with trigalaturonic acid

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Key reference

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.