PDBsum entry 4z03

Lyase

PDB id: 4z03

Contents

Protein chains

195 a.a.

Ligands

ADA-ADA-ADA

GTR-ADA-ADA ×2

MPD ×3

MRD

Metals

_CA ×8

Waters ×647

PDB id:

4z03

Name:

Lyase

Title:

C. Bescii family 3 pectate lyase double mutant k108a in complex with trigalacturonic acid

Structure:

Pectate lyase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Caldicellulosiruptor bescii (strain atcc baa- 1888 / dsm 6725 / z-1320). Organism_taxid: 521460. Strain: atcc baa-1888 / dsm 6725 / z-1320. Gene: athe_1854. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.40Å R-factor: 0.125 R-free: 0.184

Authors:

P.M.Alahuhta,V.V.Lunin

Key ref:

M.Alahuhta et al. (2015). The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. Acta Crystallogr D Biol Crystallogr, 71, 1946-1954. PubMed id: 26327384 DOI: 10.1107/S1399004715013760

Date:

25-Mar-15 Release date: 23-Dec-15

Protein chains

B9MKT4  (B9MKT4_CALBD) -  pectate lyase from Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320)

Seq: 460 a.a.

Struc: 195 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: 10.1107/S1399004715013760

Acta Crystallogr D Biol Crystallogr 71:1946-1954 (2015)

PubMed id: 26327384

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.

M.Alahuhta, L.E.Taylor, R.Brunecky, D.W.Sammond, W.Michener, M.W.Adams, M.E.Himmel, Y.J.Bomble, V.Lunin.

ABSTRACT

The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment.