9RTC | pdb_00009rtc

Okeania NrnC bound to pGG

PDB DOI: https://doi.org/10.2210/pdb9RTC/pdb
NAKB: 9RTC

Classification: HYDROLASE
Organism(s): Okenia, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-02 Released: 2026-07-15
Deposition Author(s): Mortensen, S., Burnim, A., Dufault-Thompson, K., Jiang, X., Lipka, A.E., Sondermann, H.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.298 (Depositor), 0.298 (DCC)
R-Value Work:
0.235 (Depositor), 0.234 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases.

Mortensen, S., Burnim, A.A., Dufault-Thompson, K., Lipka, A.E., Jiang, X., Sondermann, H.

(2026) Sci Adv 12: eaef1581-eaef1581

PubMed: 42585308 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aef1581
Primary Citation Related Structures:
9QRF, 9QTH, 9RTC

PubMed Abstract:
Nucleases are crucial for various bacterial processes, including genome maintenance and host defense. Deoxydinucleases (diDNases), a class of Gram-positive bacteria-specific nucleases associated with mobile genetic elements, are homologous to nanoRNase C (NrnC) in Gram-negative bacteria but exhibit notable differences: diDNases form dimers and cleave DNA dinucleotides, whereas NrnC forms octamers that process both RNA and DNA dinucleotides. The mechanism by which substrate specificity emerged, and whether it is linked to oligomerization, remained unknown. Here, we reconstructed a common ancestor of diDNases and NrnC orthologs that forms a dimer with intermediate preference for DNA. Structures of ancestral and extant dinucleases reveal gradual changes in conformation that gave rise to substrate preference, oligomeric state, and catalytic efficiency. These findings highlight how subtle, concerted structural modifications enable large-scale changes in molecular assembly and functional specialization, harnessing a conserved protein fold. DNA dinucleotide preference in the early ancestor and preservation of DNase activity in all extant enzymes strongly argue for a biological function of DNA dinucleotides.

Organizational Affiliation

CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.

Macromolecule Content

Total Structure Weight: 788.47 kDa
Atom Count: 54,470
Modeled Residue Count: 6,562
Deposited Residue Count: 6,662
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nanoRNase C	A AA B [auth N] BA [auth BB] C [auth B] A, AA, B [auth N], BA [auth BB], C [auth B], CA [auth CC], D [auth C], DA [auth DD], E [auth D], EA [auth EE], F [auth E], FA [auth FF], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O, P, Q, R, S, T, U, V, W, X, Y, Z	208	Okenia	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(PGPG)-3')	GA [auth bb], HA [auth cc], IA [auth ff]	2	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G Query on G Download:Ideal Coordinates CCD File SDF format, chain BC [auth Q] SDF format, chain BD [auth Y] SDF format, chain FB [auth H] SDF format, chain GD [auth DD] SDF format, chain HB [auth H] SDF format, chain HD [auth DD] SDF format, chain IC [auth S] SDF format, chain JA [auth A] SDF format, chain KB [auth I] SDF format, chain KC [auth T] SDF format, chain KD [auth FF] SDF format, chain MB [auth J] SDF format, chain MC [auth U] SDF format, chain PC [auth V] SDF format, chain RB [auth L] SDF format, chain SA [auth B] SDF format, chain VA [auth D] SDF format, chain VB [auth M] SDF format, chain WA [auth D] SDF format, chain WB [auth O] SDF format, chain XB [auth O] SDF format, chain XC [auth X] SDF format, chain YB [auth P] SDF format, chain YC [auth X] SDF format, chain ZA [auth E] SDF format, chain ZB [auth P] SDF format, chain YA [auth E] SDF format, chain UC [auth W] SDF format, chain TC [auth W] SDF format, chain TB [auth L] SDF format, chain TA [auth C] SDF format, chain SB [auth L] SDF format, chain RA [auth B] SDF format, chain QC [auth V] SDF format, chain QB [auth K] SDF format, chain QA [auth B] SDF format, chain PB [auth K] SDF format, chain OA [auth N] SDF format, chain NC [auth U] SDF format, chain NA [auth N] SDF format, chain LD [auth FF] SDF format, chain LC [auth T] SDF format, chain LB [auth J] SDF format, chain KA [auth A] SDF format, chain JC [auth S] SDF format, chain GB [auth H] SDF format, chain FD [auth CC] SDF format, chain FC [auth R] SDF format, chain ED [auth CC] SDF format, chain EC [auth R] SDF format, chain DD [auth Z] SDF format, chain DB [auth G] SDF format, chain CD [auth Y] SDF format, chain CB [auth G] SDF format, chain BB [auth F] SDF format, chain AD [auth Y] SDF format, chain AC [auth Q] SDF format, chain AB [auth F] MOL2 format, chain BC [auth Q] MOL2 format, chain BD [auth Y] MOL2 format, chain FB [auth H] MOL2 format, chain GD [auth DD] MOL2 format, chain HB [auth H] MOL2 format, chain HD [auth DD] MOL2 format, chain IC [auth S] MOL2 format, chain JA [auth A] MOL2 format, chain KB [auth I] MOL2 format, chain KC [auth T] MOL2 format, chain KD [auth FF] MOL2 format, chain MB [auth J] MOL2 format, chain MC [auth U] MOL2 format, chain PC [auth V] MOL2 format, chain RB [auth L] MOL2 format, chain SA [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain VB [auth M] MOL2 format, chain WA [auth D] MOL2 format, chain WB [auth O] MOL2 format, chain XB [auth O] MOL2 format, chain XC [auth X] MOL2 format, chain YB [auth P] MOL2 format, chain YC [auth X] MOL2 format, chain ZA [auth E] MOL2 format, chain ZB [auth P] MOL2 format, chain YA [auth E] MOL2 format, chain UC [auth W] MOL2 format, chain TC [auth W] MOL2 format, chain TB [auth L] MOL2 format, chain TA [auth C] MOL2 format, chain SB [auth L] MOL2 format, chain RA [auth B] MOL2 format, chain QC [auth V] MOL2 format, chain QB [auth K] MOL2 format, chain QA [auth B] MOL2 format, chain PB [auth K] MOL2 format, chain OA [auth N] MOL2 format, chain NC [auth U] MOL2 format, chain NA [auth N] MOL2 format, chain LD [auth FF] MOL2 format, chain LC [auth T] MOL2 format, chain LB [auth J] MOL2 format, chain KA [auth A] MOL2 format, chain JC [auth S] MOL2 format, chain GB [auth H] MOL2 format, chain FD [auth CC] MOL2 format, chain FC [auth R] MOL2 format, chain ED [auth CC] MOL2 format, chain EC [auth R] MOL2 format, chain DD [auth Z] MOL2 format, chain DB [auth G] MOL2 format, chain CD [auth Y] MOL2 format, chain CB [auth G] MOL2 format, chain BB [auth F] MOL2 format, chain AD [auth Y] MOL2 format, chain AC [auth Q] MOL2 format, chain AB [auth F] mmCIF format, chain BC [auth Q] mmCIF format, chain BD [auth Y] mmCIF format, chain FB [auth H] mmCIF format, chain GD [auth DD] mmCIF format, chain HB [auth H] mmCIF format, chain HD [auth DD] mmCIF format, chain IC [auth S] mmCIF format, chain JA [auth A] mmCIF format, chain KB [auth I] mmCIF format, chain KC [auth T] mmCIF format, chain KD [auth FF] mmCIF format, chain MB [auth J] mmCIF format, chain MC [auth U] mmCIF format, chain PC [auth V] mmCIF format, chain RB [auth L] mmCIF format, chain SA [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain VB [auth M] mmCIF format, chain WA [auth D] mmCIF format, chain WB [auth O] mmCIF format, chain XB [auth O] mmCIF format, chain XC [auth X] mmCIF format, chain YB [auth P] mmCIF format, chain YC [auth X] mmCIF format, chain ZA [auth E] mmCIF format, chain ZB [auth P] mmCIF format, chain YA [auth E] mmCIF format, chain UC [auth W] mmCIF format, chain TC [auth W] mmCIF format, chain TB [auth L] mmCIF format, chain TA [auth C] mmCIF format, chain SB [auth L] mmCIF format, chain RA [auth B] mmCIF format, chain QC [auth V] mmCIF format, chain QB [auth K] mmCIF format, chain QA [auth B] mmCIF format, chain PB [auth K] mmCIF format, chain OA [auth N] mmCIF format, chain NC [auth U] mmCIF format, chain NA [auth N] mmCIF format, chain LD [auth FF] mmCIF format, chain LC [auth T] mmCIF format, chain LB [auth J] mmCIF format, chain KA [auth A] mmCIF format, chain JC [auth S] mmCIF format, chain GB [auth H] mmCIF format, chain FD [auth CC] mmCIF format, chain FC [auth R] mmCIF format, chain ED [auth CC] mmCIF format, chain EC [auth R] mmCIF format, chain DD [auth Z] mmCIF format, chain DB [auth G] mmCIF format, chain CD [auth Y] mmCIF format, chain CB [auth G] mmCIF format, chain BB [auth F] mmCIF format, chain AD [auth Y] mmCIF format, chain AC [auth Q] mmCIF format, chain AB [auth F]	AB [auth F] AC [auth Q] AD [auth Y] BB [auth F] BC [auth Q] AB [auth F], AC [auth Q], AD [auth Y], BB [auth F], BC [auth Q], BD [auth Y], CB [auth G], CD [auth Y], DB [auth G], DD [auth Z], EC [auth R], ED [auth CC], FB [auth H], FC [auth R], FD [auth CC], GB [auth H], GD [auth DD], HB [auth H], HD [auth DD], IC [auth S], JA [auth A], JC [auth S], KA [auth A], KB [auth I], KC [auth T], KD [auth FF], LB [auth J], LC [auth T], LD [auth FF], MB [auth J], MC [auth U], NA [auth N], NC [auth U], OA [auth N], PB [auth K], PC [auth V], QA [auth B], QB [auth K], QC [auth V], RA [auth B], RB [auth L], SA [auth B], SB [auth L], TA [auth C], TB [auth L], TC [auth W], UC [auth W], VA [auth D], VB [auth M], WA [auth D], WB [auth O], XB [auth O], XC [auth X], YA [auth E], YB [auth P], YC [auth X], ZA [auth E], ZB [auth P]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain AB [auth F] Focus chain AC [auth Q] Focus chain AD [auth Y] Focus chain BB [auth F] Focus chain BC [auth Q] Focus chain BD [auth Y] Focus chain CB [auth G] Focus chain CD [auth Y] Focus chain DB [auth G] Focus chain DD [auth Z] Focus chain EC [auth R] Focus chain ED [auth CC] Focus chain FB [auth H] Focus chain FC [auth R] Focus chain FD [auth CC] Focus chain GB [auth H] Focus chain GD [auth DD] Focus chain HB [auth H] Focus chain HD [auth DD] Focus chain IC [auth S] Focus chain JA [auth A] Focus chain JC [auth S] Focus chain KA [auth A] Focus chain KB [auth I] Focus chain KC [auth T] Focus chain KD [auth FF] Focus chain LB [auth J] Focus chain LC [auth T] Focus chain LD [auth FF] Focus chain MB [auth J] Focus chain MC [auth U] Focus chain NA [auth N] Focus chain NC [auth U] Focus chain OA [auth N] Focus chain PB [auth K] Focus chain PC [auth V] Focus chain QA [auth B] Focus chain QB [auth K] Focus chain QC [auth V] Focus chain RA [auth B] Focus chain RB [auth L] Focus chain SA [auth B] Focus chain SB [auth L] Focus chain TA [auth C] Focus chain TB [auth L] Focus chain TC [auth W] Focus chain UC [auth W] Focus chain VA [auth D] Focus chain VB [auth M] Focus chain WA [auth D] Focus chain WB [auth O] Focus chain XB [auth O] Focus chain XC [auth X] Focus chain YA [auth E] Focus chain YB [auth P] Focus chain YC [auth X] Focus chain ZA [auth E] Focus chain ZB [auth P] Interactions & Density Focus chain AB [auth F] Focus chain AC [auth Q] Focus chain AD [auth Y] Focus chain BB [auth F] Focus chain BC [auth Q] Focus chain BD [auth Y] Focus chain CB [auth G] Focus chain CD [auth Y] Focus chain DB [auth G] Focus chain DD [auth Z] Focus chain EC [auth R] Focus chain ED [auth CC] Focus chain FB [auth H] Focus chain FC [auth R] Focus chain FD [auth CC] Focus chain GB [auth H] Focus chain GD [auth DD] Focus chain HB [auth H] Focus chain HD [auth DD] Focus chain IC [auth S] Focus chain JA [auth A] Focus chain JC [auth S] Focus chain KA [auth A] Focus chain KB [auth I] Focus chain KC [auth T] Focus chain KD [auth FF] Focus chain LB [auth J] Focus chain LC [auth T] Focus chain LD [auth FF] Focus chain MB [auth J] Focus chain MC [auth U] Focus chain NA [auth N] Focus chain NC [auth U] Focus chain OA [auth N] Focus chain PB [auth K] Focus chain PC [auth V] Focus chain QA [auth B] Focus chain QB [auth K] Focus chain QC [auth V] Focus chain RA [auth B] Focus chain RB [auth L] Focus chain SA [auth B] Focus chain SB [auth L] Focus chain TA [auth C] Focus chain TB [auth L] Focus chain TC [auth W] Focus chain UC [auth W] Focus chain VA [auth D] Focus chain VB [auth M] Focus chain WA [auth D] Focus chain WB [auth O] Focus chain XB [auth O] Focus chain XC [auth X] Focus chain YA [auth E] Focus chain YB [auth P] Focus chain YC [auth X] Focus chain ZA [auth E] Focus chain ZB [auth P]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OC [auth U] MOL2 format, chain OC [auth U] mmCIF format, chain OC [auth U]	OC [auth U]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OC [auth U] Interactions & Density Focus chain OC [auth U]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CC [auth Q] SDF format, chain DC [auth Q] SDF format, chain GC [auth R] SDF format, chain HC [auth R] SDF format, chain ID [auth EE] SDF format, chain JB [auth H] SDF format, chain JD [auth EE] SDF format, chain MA [auth A] SDF format, chain MD [auth FF] SDF format, chain ND [auth FF] SDF format, chain PA [auth N] SDF format, chain ZC [auth X] SDF format, chain XA [auth D] SDF format, chain WC [auth W] SDF format, chain VC [auth W] SDF format, chain UB [auth L] SDF format, chain UA [auth C] SDF format, chain SC [auth V] SDF format, chain RC [auth V] SDF format, chain OB [auth J] SDF format, chain NB [auth J] SDF format, chain LA [auth A] SDF format, chain IB [auth H] SDF format, chain EB [auth G] MOL2 format, chain CC [auth Q] MOL2 format, chain DC [auth Q] MOL2 format, chain GC [auth R] MOL2 format, chain HC [auth R] MOL2 format, chain ID [auth EE] MOL2 format, chain JB [auth H] MOL2 format, chain JD [auth EE] MOL2 format, chain MA [auth A] MOL2 format, chain MD [auth FF] MOL2 format, chain ND [auth FF] MOL2 format, chain PA [auth N] MOL2 format, chain ZC [auth X] MOL2 format, chain XA [auth D] MOL2 format, chain WC [auth W] MOL2 format, chain VC [auth W] MOL2 format, chain UB [auth L] MOL2 format, chain UA [auth C] MOL2 format, chain SC [auth V] MOL2 format, chain RC [auth V] MOL2 format, chain OB [auth J] MOL2 format, chain NB [auth J] MOL2 format, chain LA [auth A] MOL2 format, chain IB [auth H] MOL2 format, chain EB [auth G] mmCIF format, chain CC [auth Q] mmCIF format, chain DC [auth Q] mmCIF format, chain GC [auth R] mmCIF format, chain HC [auth R] mmCIF format, chain ID [auth EE] mmCIF format, chain JB [auth H] mmCIF format, chain JD [auth EE] mmCIF format, chain MA [auth A] mmCIF format, chain MD [auth FF] mmCIF format, chain ND [auth FF] mmCIF format, chain PA [auth N] mmCIF format, chain ZC [auth X] mmCIF format, chain XA [auth D] mmCIF format, chain WC [auth W] mmCIF format, chain VC [auth W] mmCIF format, chain UB [auth L] mmCIF format, chain UA [auth C] mmCIF format, chain SC [auth V] mmCIF format, chain RC [auth V] mmCIF format, chain OB [auth J] mmCIF format, chain NB [auth J] mmCIF format, chain LA [auth A] mmCIF format, chain IB [auth H] mmCIF format, chain EB [auth G]	CC [auth Q] DC [auth Q] EB [auth G] GC [auth R] HC [auth R] CC [auth Q], DC [auth Q], EB [auth G], GC [auth R], HC [auth R], IB [auth H], ID [auth EE], JB [auth H], JD [auth EE], LA [auth A], MA [auth A], MD [auth FF], NB [auth J], ND [auth FF], OB [auth J], PA [auth N], RC [auth V], SC [auth V], UA [auth C], UB [auth L], VC [auth W], WC [auth W], XA [auth D], ZC [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CC [auth Q] Focus chain DC [auth Q] Focus chain EB [auth G] Focus chain GC [auth R] Focus chain HC [auth R] Focus chain IB [auth H] Focus chain ID [auth EE] Focus chain JB [auth H] Focus chain JD [auth EE] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain MD [auth FF] Focus chain NB [auth J] Focus chain ND [auth FF] Focus chain OB [auth J] Focus chain PA [auth N] Focus chain RC [auth V] Focus chain SC [auth V] Focus chain UA [auth C] Focus chain UB [auth L] Focus chain VC [auth W] Focus chain WC [auth W] Focus chain XA [auth D] Focus chain ZC [auth X] Interactions & Density Focus chain CC [auth Q] Focus chain DC [auth Q] Focus chain EB [auth G] Focus chain GC [auth R] Focus chain HC [auth R] Focus chain IB [auth H] Focus chain ID [auth EE] Focus chain JB [auth H] Focus chain JD [auth EE] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain MD [auth FF] Focus chain NB [auth J] Focus chain ND [auth FF] Focus chain OB [auth J] Focus chain PA [auth N] Focus chain RC [auth V] Focus chain SC [auth V] Focus chain UA [auth C] Focus chain UB [auth L] Focus chain VC [auth W] Focus chain WC [auth W] Focus chain XA [auth D] Focus chain ZC [auth X]