PDBsum entry 5amv

Lyase

PDB id

5amv

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Contents

			Protein chain

					399 a.a.

			Ligands

					ADA-ADA-ADA


					ACT


					GOL

			Metals

					_CA

			Waters ×592

PDB id:

5amv

Links

Name:

Lyase

Title:

Structural insights into the loss of catalytic competence in pectate lyase at low ph

Structure:

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

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss

Resolution:

1.57Å

R-factor:

0.161

R-free:

0.193

Authors:

S.C.M.Teixeira,S.Ali,C.Sondergaard,R.Pickersgill

Key ref:

S.Ali et al. (2015). Structural insights into the loss of catalytic competence in pectate lyase activity at low pH. Febs Lett, 589, 3242-3246. PubMed id: 26420545 DOI: 10.1016/j.febslet.2015.09.014

Date:

02-Sep-15

Release date:

30-Sep-15

PROCHECK

	Headers

	References

Protein chain

P39116 (PLY_BACSU) - Pectate lyase from Bacillus subtilis (strain 168)

Seq: Struc:					420 a.a. 399 a.a.

Key:

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.4.2.2.2 - pectate lyase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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: 10.1016/j.febslet.2015.09.014	Febs Lett 589:3242-3246 (2015)
PubMed id: 26420545

Structural insights into the loss of catalytic competence in pectate lyase activity at low pH.
S.Ali, C.R.Søndergaard, S.Teixeira, R.W.Pickersgill.

ABSTRACT

Pectate lyase, a family 1 polysaccharide lyase, catalyses cleavage of the α-1,4 linkage of the polysaccharide homogalacturonan via an anti β-elimination reaction. In the Michaelis complex two calcium ions bind between the C6 carboxylate of the d-galacturonate residue and enzyme aspartates at the active centre (+1 subsite), they withdraw electrons acidifying the C5 proton facilitating its abstraction by the catalytic arginine. Here we show that activity is lost at low pH because protonation of aspartates results in the loss of the two catalytic calcium-ions causing a profound failure to correctly organise the Michaelis complex.