PDBsum entry: 3gze

Hydrolase

PDB id: 3gze

Contents

Protein chains

213 a.a. *

186 a.a. *

Ligands

PRO-SER-PRO-SER-PRO-SER

PRO-SER-PRO-SER-PRO-SER-PRO-SER

ACY ×5

Metals

_ZN ×14

Waters ×468

* Residue conservation analysis

PDB id:

3gze

Name:

Hydrolase

Title:

Algal prolyl 4-hydroxylase complexed with zinc and (ser-pro) substrate

Structure:

Predicted protein. Chain: a, b, c, d. Fragment: n-terminally truncated construct, residues 30-251 synonym: prolyl 4-hydroxylase. Engineered: yes. Peptide substrate (ser-pro)5. Chain: x, y. Engineered: yes

Source:

Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: wild type cc125 mt+ 137c. Gene: p4h-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this is designed using the (ser-pro)n -regio potential substrate of cr-p4h-1, namely the domain 3 of the

Resolution:

1.98Å R-factor: 0.219 R-free: 0.254

Authors:

M.K.Koski,R.K.Wierenga

Key ref:

M.K.Koski et al. (2009). The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif. J Biol Chem, 284, 25290-25301. PubMed id: 19553701 DOI: 10.1074/jbc.M109.014050

Date:

07-Apr-09 Release date: 23-Jun-09

Protein chains

A8J7D3  (A8J7D3_CHLRE) -  Predicted protein

Seq: 297 a.a.

Struc: 213 a.a.

Protein chains

A8J7D3  (A8J7D3_CHLRE) -  Predicted protein

Seq: 297 a.a.

Struc: 186 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (1 term)
• Biochemical function: oxidoreductase activity (5 terms)

DOI no: 10.1074/jbc.M109.014050

J Biol Chem 284:25290-25301 (2009)

PubMed id: 19553701

The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif.

M.K.Koski, R.Hieta, M.Hirsilä, A.Rönkä, J.Myllyharju, R.K.Wierenga.

ABSTRACT

Plant and algal prolyl 4-hydroxylases (P4Hs) are key enzymes in the synthesis of cell wall components. These monomeric enzymes belong to the 2-oxoglutarate dependent superfamily of enzymes characterized by a conserved jelly-roll framework. This algal P4H has high sequence similarity to the catalytic domain of the vertebrate, tetrameric collagen P4Hs, whereas there are distinct sequence differences with the oxygen-sensing hypoxia-inducible factor P4H subfamily of enzymes. We present here a 1.98-A crystal structure of the algal Chlamydomonas reinhardtii P4H-1 complexed with Zn(2+) and a proline-rich (Ser-Pro)(5) substrate. This ternary complex captures the competent mode of binding of the peptide substrate, being bound in a left-handed (poly)l-proline type II conformation in a tunnel shaped by two loops. These two loops are mostly disordered in the absence of the substrate. The importance of these loops for the function is confirmed by extensive mutagenesis, followed up by enzyme kinetic characterizations. These loops cover the central Ser-Pro-Ser tripeptide of the substrate such that the hydroxylation occurs in a highly buried space. This novel mode of binding does not depend on stacking interactions of the proline side chains with aromatic residues. Major conformational changes of the two peptide binding loops are predicted to be a key feature of the catalytic cycle. These conformational changes are probably triggered by the conformational switch of Tyr(140), as induced by the hydroxylation of the proline residue. The importance of these findings for understanding the specific binding and hydroxylation of (X-Pro-Gly)(n) sequences by collagen P4Hs is also discussed.

Selected figure(s)

Figure 2.
Stereoview of the (2F[o]-F[c])α[c] omit density (countered at 1 σ) for the (Ser-Pro)[5] in molecule C of the Cr-P4H-1 crystal structure. The active site with Zn^2+, coordinated by His^143, Asp^145, His^227 and an acetate molecule (green sticks), and some of the most important (Ser-Pro)[5] binding residues are shown. Hydrogen bonds are indicated by dashed lines.

Figure 9.
The down-puckered Pro^6 of (Ser-Pro)[5] at the active site of the Zn-peptide complex with its (2F[o]-F[c])α[c] omit density (countered at 1σ). The figure also includes a superimposed up-puckered 4-R-hydroxyproline residue (magenta bond colors), which is the product of the P4H reaction (PDB ID 2D3F). The side chain of Tyr^140, which will clash with the product, is also shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 25290-25301) copyright 2009.

Figures were selected by the author.