6B9V

Crystal Structure of a New Diphosphatase from the PhnP Family

PDB DOI: https://doi.org/10.2210/pdb6B9V/pdb

Classification: HYDROLASE
Organism(s): Candidatus Koribacter versatilis Ellin345
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-10-11 Released: 2018-10-17
Deposition Author(s): Li, Q., Bruner, S.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.196
R-Value Work: 0.159
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

An unusual diphosphatase from the PhnP family cleaves reactive FAD photoproducts.

Beaudoin, G.A.W., Li, Q., Bruner, S.D., Hanson, A.D.

(2018) Biochem J 475: 261-272

PubMed: 29229761 Search on PubMed
DOI: https://doi.org/10.1042/BCJ20170817
Primary Citation of Related Structures:
6B9V

PubMed Abstract:
Flavins are notoriously photolabile, but while the photoproducts derived from the iso -alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family. The representative PhnP family enzyme from Koribacter versatilis (here named Fpd, F AD p hotoproduct d iphosphatase) was found to have high, Mn ²⁺-dependent diphosphatase activity against FAD photoproducts, FAD, and ADP-ribose, but almost no phosphodiesterase activity against riboflavin 4',5'-cyclic phosphate, a chemical breakdown product of FAD. To provide a structural basis of the unique Fpd activity, the crystal structure of K. versatilis Fpd was determined. The results place Fpd in the broad metallo-β-lactamase-like family of hydrolases, a diverse family commonly using two metals for hydrolytic catalysis. The active site of Fpd contains two Mn ²⁺ ions and a bound phosphate, consistent with a diphosphatase mechanism. Our results characterize the first PhnP family member that is a diphosphatase rather than a cyclic phosphodiesterase and suggest its involvement in a cellular damage-control system that efficiently hydrolyzes the reactive, ADP-ribose-like products of FAD photodegradation.

Organizational Affiliation

Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A.

Macromolecule Content

Total Structure Weight: 61.77 kDa
Atom Count: 4,377
Modelled Residue Count: 507
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase-like protein	A, B	271	Candidatus Koribacter versatilis Ellin345	Mutation(s): 0 Gene Names: Acid345_2630
UniProt
Find proteins for Q1INB9 (Koribacter versatilis (strain Ellin345)) Explore Q1INB9 Go to UniProtKB: Q1INB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1INB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.196
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.78	α = 90
b = 41.364	β = 95.2
c = 96.034	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Li, Q.

Bruner, S.D.

Funding Organization	Location	Grant Number
	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description