PDBsum entry: 1ru4

Lyase

PDB id: 1ru4

Contents

Protein chain

400 a.a. *

Metals

_CA ×2

Waters ×552

* Residue conservation analysis

PDB id:

1ru4

Name:

Lyase

Title:

Crystal structure of pectate lyase pel9a

Structure:

Pectate lyase. Chain: a. Synonym: pel9a. Engineered: yes

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Gene: pell. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.167 R-free: 0.186

Authors:

J.Jenkins,V.E.Shevchik,N.Hugouvieux-Cotte-Pattat, R.W.Pickersgill

Key ref:

J.Jenkins et al. (2004). The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem, 279, 9139-9145. PubMed id: 14670977 DOI: 10.1074/jbc.M311390200

Date:

11-Dec-03 Release date: 13-Apr-04

Protein chain

P0C1A6  (PLYL_ERWCH) -  Pectate lyase L

Seq: 425 a.a.

Struc: 400 a.a.*

* PDB and UniProt seqs differ at 21 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.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1074/jbc.M311390200

J Biol Chem 279:9139-9145 (2004)

PubMed id: 14670977

The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.

J.Jenkins, V.E.Shevchik, N.Hugouvieux-Cotte-Pattat, R.W.Pickersgill.

ABSTRACT

The "family 9 polysaccharide lyase" pectate lyase L (Pel9A) from Erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. Pel9A has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family Pel1A pectate lyases, and there is strong evidence for a common second calcium ion that binds between enzyme and substrate in the "Michaelis" complex. Although the primary calcium ion binds substrate in subsite -1, it is the second calcium ion, whose binding site is formed by the coming together of enzyme and substrate, that facilitates abstraction of the C5 proton from the sacharride in subsite +1. The role of the second calcium is to withdraw electrons from the C6 carboxylate of the substrate, thereby acidifying the C5 proton facilitating its abstraction and resulting in an E1cb-like anti-beta-elimination mechanism. The active site geometries and mechanism of Pel1A and Pel9A are closely similar, but the catalytic base is a lysine in the Pel9A enzymes as opposed to an arginine in the Pel1A enzymes.

Selected figure(s)

Figure 2.
FIG. 2. Distinct side chain stacks within the parallel -helix domain of Pel9A. a, an all atom representation of coil 5 of the superhelical architecture of Pel9A formed by residues 211-234, with PB1, PB2, and PB3 labeled and viewed normal to the -strands. Phe-211 and Asn-231 contribute to the aromatic stack and the hydrogen-bonded asparagine-ladder, respectively, within the T3 turn in Pel9A. b, consecutive coils of Pel9A showing like-on-like stacks involving asparagines 198, 231, 255, and 293 and phenylalanines 211, 236, 272, and 298. c, residues 226-248 of Pel1A (coil 4 of BsPel) viewed normal to the -strands. Residues 240 and 242 contribute to the asparagine ladder and to the aromatic stack, respectively, of the Pel1A enzymes. d, consecutive coils of Pel1A showing the aromatic stack on PB3 and the asparagine ladder within the T2 turn. Alanine is at the position corresponding to the aromatic stack of Pel1A in Pel9A (195, 228, 252, 290) to accommodate the aromatic stack on the interior of PB1.

Figure 3.
FIG. 3. The calcium-binding sites of Pel9A and Pel1A. a, anomalous difference Fourier map (chicken wire mesh) revealing the presence of a metal bound to Pel9A by aspartates 209, 233, and 237 (Asp-234 is also a calcium-ligand, not shown). The putative catalytic base, lysine 273, is also shown. b, calcium-binding site of Pel1A (BsPel) showing calcium bound by aspartates 184, 223, and 227. The catalytic base, arginine 279, is also shown. c, substrate binding to Pel1A (PelC coordinates kindly provided by Prof. Fran Jurnak). Galacturonates occupying subsites -1 (left) and +1 (right) are shown together with four calcium-binding sites (ligands for sites three and four are not shown). d, substrate modeled in to the active center of Pel9A. The primary calcium-binding site is strikingly similar to that of Pel1A (BsPel). The second calcium site is anticipated to bind the complex at a similar position (as suggested by the Pb2 site), and the third and fourth sites will be different if they exist in Pel9A. Phenylalanine 239 in Pel9A forms a platform for the galacturonate in subsite -1. This figure was prepared using BOBSCRIPT (2).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9139-9145) copyright 2004.

Figures were selected by an automated process.