PDBsum entry: 2o1d

Lyase

PDB id: 2o1d

Contents

Protein chain

399 a.a. *

Ligands

ADA-ADA-ADA

Metals

_CA ×3

Waters ×595

* Residue conservation analysis

PDB id:

2o1d

Name:

Lyase

Title:

Pectate lyase bound to trisaccharide

Structure:

Pectate lyase. Chain: a. Synonym: pl. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: pel. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.150 R-free: 0.199

Authors:

R.W.Pickersgill,A.Seyedarabi

Key ref:

A.Seyedarabi et al. (2010). Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase. Biochemistry, 49, 539-546. PubMed id: 20000851 DOI: 10.1021/bi901503g

Date:

28-Nov-06 Release date: 20-Nov-07

Protein chain

P39116  (PLY_BACSU) -  Pectate lyase

Seq: 420 a.a.

Struc: 399 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biochemical function: lyase activity (3 terms)

DOI no: 10.1021/bi901503g

Biochemistry 49:539-546 (2010)

PubMed id: 20000851

Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase.

A.Seyedarabi, T.T.To, S.Ali, S.Hussain, M.Fries, R.Madsen, M.H.Clausen, S.Teixteira, K.Brocklehurst, R.W.Pickersgill.

ABSTRACT

Pectate lyases harness anti beta-elimination chemistry to cleave the alpha-1,4 linkage in the homogalacturonan region of plant cell wall pectin. We have studied the binding of five pectic oligosaccharides to Bacillus subtilis pectate lyase in crystals of the inactive enzyme in which the catalytic base is substituted with alanine (R279A). We discover that the three central subsites (-1, +1, and +2) have a profound preference for galacturonate but that the distal subsites can accommodate methylated galacturonate. It is reasonable to assume therefore that pectate lyase can cleave pectin with three consecutive galacturonate residues. The enzyme in the absence of substrate binds a single calcium ion, and we show that two additional calcium ions bind between enzyme and substrate carboxylates occupying the +1 subsite in the Michaelis complex. The substrate binds less intimately to the enzyme in a complex made with a catalytic base in place but in the absence of the calcium ions and an adjacent lysine. In this complex, the catalytic base is correctly positioned to abstract the C5 proton, but there are no calcium ions binding the carboxylate at the +1 subsite. It is clear, therefore, that the catalytic calcium ions and adjacent lysine promote catalysis by acidifying the alpha-proton, facilitating its abstraction by the base. There is also clear evidence that binding distorts the relaxed 2(1) or 3(1) helical conformation of the oligosaccharides in the region of the scissile bond.