2X66

The binary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway) and cyanide

Summary for 2X66

• Entry DOI: 10.2210/pdb2x66/pdb
• Related: 2V7I 2V7J 2V7K 2V7L 2V7M 2X67 2X68
• Descriptor: PRNB, CYANIDE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• Functional Keywords: biosynthetic protein, indolamine/tryptophan dioxygenase superfamily
• Biological source: PSEUDOMONAS FLUORESCENS
• Total number of polymer chains: 1
• Total formula weight: 40656.06

Authors

Zhu, X.,van pee, K.-H.,Naismith, J.H. (deposition date: 2010-02-15, release date: 2010-03-02, Last modification date: 2023-12-20)

Primary citation

Zhu, X.,Van Pee, K.-H.,Naismith, J.H.
The Ternary Complex of Prnb (the Second Enzyme in Pyrrolnitrin Biosynthesis Pathway), Tryptophan and Cyanide Yields New Mechanistic Insights Into the Indolamine Dioxygenase Superfamily.
J.Biol.Chem., 285:21126-, 2010

PubMed Abstract: Pyrrolnitrin (3-chloro-4-(2'-nitro-3'-chlorophenyl)pyrrole) is a broad-spectrum antifungal compound isolated from Pseudomonas pyrrocinia. Four enzymes (PrnA, PrnB, PrnC, and PrnD) are required for pyrrolnitrin biosynthesis from tryptophan. PrnB rearranges the indole ring of 7-Cl-l-tryptophan and eliminates the carboxylate group. PrnB shows robust activity in vivo, but in vitro activity for PrnB under defined conditions remains undetected. The structure of PrnB establishes that the enzyme belongs to the heme b-dependent indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) family. We report the cyanide complex of PrnB and two ternary complexes with both l-tryptophan or 7-Cl-l-tryptophan and cyanide. The latter two complexes are essentially identical and mimic the likely catalytic ternary complex that occurs during turnover. In the cyanide ternary complexes, a loop previously disordered becomes ordered, contributing to the binding of substrates. The conformations of the bound tryptophan substrates are changed from that seen previously in the binary complexes. In l-tryptophan ternary complex, the indole ring now adopts the same orientation as seen in the PrnB binary complexes with other tryptophan substrates. The amide and carboxylate group of the substrate are orientated in a new conformation. Tyr(321) and Ser(332) play a key role in binding these groups. The structures suggest that catalysis requires an l-configured substrate. Isothermal titration calorimetry data suggest d-tryptophan does not bind after cyanide (or oxygen) coordinates with the distal (or sixth) site of heme. This is the first ternary complex with a tryptophan substrate of a member of the tryptophan dioxygenase superfamily and has mechanistic implications.

PubMed: 20421301
DOI: 10.1074/JBC.M110.120485

Experimental method

X-RAY DIFFRACTION (2.09 Å)