7LFQ | pdb_00007lfq

Pyrococcus RNA ligase

• PDB DOI: https://doi.org/10.2210/pdb7LFQ/pdb
• NAKB: 7LFQ

• Classification: LIGASE/DNA
• Organism(s): Pyrococcus horikoshii, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-01-18 Released: 2021-03-03 
• Deposition Author(s): Goldgur, Y., Shuman, S., Banerjee, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide.

Banerjee, A., Goldgur, Y., Shuman, S.

(2021) RNA 27: 584-590

• PubMed: 33619169 
• DOI: https://doi.org/10.1261/rna.078692.121
• Primary Citation Related Structures: 
  7LFQ


• PubMed Abstract: 
  

  RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)-GMP, RNA 3'-phosphate, and RNA3'pp5'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. Here we report a 2.7 Å crystal structure of Pyrococcus horikoshii RtcB in complex with a 6-mer 5'-OH DNA oligonucleotide _HO A ¹ pT ² pG ³ pT ⁴ pC ⁵ pC ⁶ , which reveals enzymic contacts of Asn202 to the terminal 5'-OH nucleophile; Arg238 to the A ¹ pT ² and T ² pG ³ phosphates; Arg190 and Gln194 to the T ² pG ³ phosphate; and an Arg190 π-cation interaction with the G3 nucleobase. The structural insights affirm functional studies of E. coli RtcB that implicated the conserved counterpart of Arg238 in engagement of the 5'-OH strand for ligation. The essential active site Cys98 that coordinates two manganese ions is oxidized to cysteine sulfonic acid in our structure, raising the prospect that RtcB activity might be sensitive to modulation during oxidative stress.

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Organizational Affiliation: 
• Sloan Kettering Institute.
Sloan Kettering Institute [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.72 kDa 
• Atom Count: 3,910 
• Modeled Residue Count: 487 
• Deposited Residue Count: 507 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-splicing ligase RtcB	A	501	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: rtcB, PH1602 EC: 6.5.1.8 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for O59245 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59245  Go to UniProtKB:  O59245

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*CP*C)-3')	B	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.379	α = 90
b = 151.379	β = 90
c = 82.337	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Goldgur, Y., Shuman, S., Banerjee, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM126945

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 2.0: 2022-06-29
  Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2022-12-07
  Changes: Database references
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.3: 2023-11-15
  Changes: Data collection