PDBsum entry 6d2c

Lyase

PDB id: 6d2c

Contents

Protein chains

260 a.a.

Ligands

PO4 ×4

EDO ×2

Metals

_CA ×2

Waters ×710

PDB id:

6d2c

Name:

Lyase

Title:

Structure of ulvan lyase from nonlaben ulvanivorans- nlr48

Structure:

Ulvan lyase. Chain: a, b. Engineered: yes

Source:

Nonlabens ulvanivorans. Organism_taxid: 906888. Gene: il45_01530. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.91Å R-factor: 0.170 R-free: 0.201

Authors:

T.Ulaganathan,M.Cygler

Key ref:

T.Ulaganathan et al. (2018). Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans. J Biol Chem, 293, 11564-11573. PubMed id: 29875159 DOI: 10.1074/jbc.RA118.003659

Date:

13-Apr-18 Release date: 06-Jun-18

Protein chains

A0A084JZF2  (UL28B_NONUL) -  Ulvan lyase NLR48 from Nonlabens ulvanivorans

Seq: 303 a.a.

Struc: 260 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.2.- - ?????

DOI no: 10.1074/jbc.RA118.003659

J Biol Chem 293:11564-11573 (2018)

PubMed id: 29875159

Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans.

T.Ulaganathan, E.Banin, W.Helbert, M.Cygler.

ABSTRACT

Ulvan is a complex sulfated polysaccharide present in the cell wall of green algae of the genus Ulva (Chlorophyta). The first ulvan-degrading polysaccharide lyases were identified several years ago, and more were discovered through genome sequencing of marine bacteria. Ulvan lyases are now grouped in three polysaccharide lyase (PL) families in the CAZy database, PL24, PL25, and PL28. The recently determined structures of the representative lyases from families PL24 and PL25 show that they adopt a seven-bladed β-propeller fold and utilize the His/Tyr catalytic mechanism. No structural information is yet available for PL28 ulvan lyases. NLR48 from Nonlabens ulvanivorans belongs to PL28 together with its close paralog, NLR42. Biochemical studies of NLR42 have revealed that it can cleave ulvan next to both uronic acid epimers. We report the crystal structure of ulvan lyase NLR48 at 1.9-Å resolution. It has a β-jelly roll fold with an extended, deep, and positively charged substrate-binding cleft. Putative active-site residues were identified from the sequence conservation pattern, and their role was confirmed by site-directed mutagenesis. The structure of an inactive K162M mutant with a tetrasaccharide substrate showed the substrate occupying the "-" subsites. Comparison with lyases from other PL families with β-jelly roll folds supported assignment of the active site and explained its ability to degrade ulvan next to either epimer of uronic acid. NLR48 contains the His/Tyr catalytic machinery with Lys¹⁶² and Tyr²⁸¹ playing the catalytic base/acid roles.