9EMG | pdb_00009emg

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate as a product of c-di-GMP cleavage

PDB DOI: https://doi.org/10.2210/pdb9EMG/pdb

Classification: HYDROLASE
Organism(s): Stenotrophomonas maltophilia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-08 Released: 2024-12-25
Deposition Author(s): Adamkova, K., Koval, T., Kolenko, P., Dohnalek, J.
Funding Organization(s): Czech Science Foundation, Czech Academy of Sciences, Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.131 (Depositor), 0.114 (DCC)
R-Value Work:
0.111 (Depositor), 0.114 (DCC)
R-Value Observed:
0.113 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study.

Adamkova, K., Trundova, M., Koval, T., Hustakova, B., Kolenko, P., Duskova, J., Skalova, T., Dohnalek, J.

(2025) FEBS J 292: 129-152

PubMed: 39361520 Search on PubMed
DOI: https://doi.org/10.1111/febs.17265
Primary Citation of Related Structures:
8QJL, 8QJM, 8QJN, 8QJO, 8QJP, 8QJQ, 9EMG

PubMed Abstract:
Nucleases of the S1/P1 family have important applications in biotechnology and molecular biology. We have performed structural analyses of SmNuc1 nuclease from Stenotrophomonas maltophilia, including RNA cleavage product binding and mutagenesis in a newly discovered flexible Arg74-motif, involved in substrate binding and product release and likely contributing to the high catalytic rate. The Arg74Gln mutation shifts substrate preference towards RNA. Purine nucleotide binding differs compared to pyrimidines, confirming the plasticity of the active site. The enzyme-product interactions indicate a gradual, stepwise product release. The activity of SmNuc1 towards c-di-GMP in crystal resulted in a distinguished complex with the emerging product 5'-GMP. This enzyme from an opportunistic pathogen relies on specific architecture enabling high performance under broad conditions, attractive for biotechnologies.

Organizational Affiliation

Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.

Macromolecule Content

Total Structure Weight: 58.52 kDa
Atom Count: 4,999
Modeled Residue Count: 496
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1/P1 nuclease	A, B	254	Stenotrophomonas maltophilia	Mutation(s): 0 Gene Names: FEO86_17535, HKK60_04680, I5U85_21415 EC: 3.1.30.1
UniProt
Find proteins for B2FSF8 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FSF8 Go to UniProtKB: B2FSF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2FSF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	I [auth A] J [auth A] K [auth A] Q [auth B] R [auth B] I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	F [auth A], G [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] L [auth B] M [auth B] C [auth A], D [auth A], E [auth A], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.131 (Depositor), 0.114 (DCC)
R-Value Work: 0.111 (Depositor), 0.114 (DCC)
R-Value Observed: 0.113 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.34	α = 90
b = 72.637	β = 102.098
c = 82.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	23-06295S
Czech Academy of Sciences	Czech Republic	86652036
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023042
European Regional Development Fund	European Union	CZ.02.1.01/0.0/18_046/0015974