5C7Q | pdb_00005c7q

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

PDB DOI: https://doi.org/10.2210/pdb5C7Q/pdb

Classification: HYDROLASE
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2015-06-24 Released: 2016-01-20
Deposition Author(s): Gabelli, S.B., de la Pena, A.H., Suarez, A., Amzel, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.215 (Depositor), 0.223 (DCC)
R-Value Work:
0.186 (Depositor), 0.198 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.

de la Pena, A.H., Suarez, A., Duong-Ly, K.C., Schoeffield, A.J., Pizarro-Dupuy, M.A., Zarr, M., Pineiro, S.A., Amzel, L.M., Gabelli, S.B.

(2015) PLoS One 10: e0141716-e0141716

PubMed: 26524597 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0141716
Primary Citation Related Structures:
5C7Q, 5C7T, 5C8L

PubMed Abstract:
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.

Organizational Affiliation

Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America; Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

Macromolecule Content

Total Structure Weight: 44.74 kDa
Atom Count: 3,497
Modeled Residue Count: 362
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NudF protein	A, B	182	Bdellovibrio bacteriovorus HD100	Mutation(s): 0 Gene Names: nudF, Bd3179 EC: 3.6.1.13
UniProt
Find proteins for Q6MIH8 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MIH8 Go to UniProtKB: Q6MIH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MIH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A]	M [auth A], W [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain W [auth B]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain L [auth A]	L [auth A], V [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain V [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] N [auth A] O [auth A] C [auth A], D [auth A], E [auth A], N [auth A], O [auth A], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] Q [auth B] F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]