2HVR | pdb_00002hvr

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick

• PDB DOI: https://doi.org/10.2210/pdb2HVR/pdb
• NAKB: 2HVR

• Classification: LIGASE/RNA/DNA
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-07-30 Released: 2006-10-17 
• Deposition Author(s): Nandakumar, J., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.295 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.238 (DCC) 

Starting Model: experimental

Literature

RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward.

Nandakumar, J., Shuman, S., Lima, C.D.

(2006) Cell 127: 71-84

• PubMed: 17018278 
• DOI: https://doi.org/10.1016/j.cell.2006.08.038
• Primary Citation Related Structures: 
  2HVQ, 2HVR, 2HVS


• PubMed Abstract: 
  

  T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.

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Organizational Affiliation: 
• Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 106.16 kDa 
• Atom Count: 7,219 
• Modeled Residue Count: 736 
• Deposited Residue Count: 768 
• Unique protein chains: 1
• Unique nucleic acid chains: 1
• Unique hybrid chains: 2

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T4 RNA ligase 2	G [auth A], H [auth B]	335	Tequatrovirus T4	Mutation(s): 0  Gene Names: Y10A, 24.1 EC: 6.5.1.3
UniProt
Find proteins for P32277 (Enterobacteria phage T4) Explore P32277  Go to UniProtKB:  P32277

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3'	A [auth C], D [auth F]	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'	B [auth D], E [auth G]	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(P*A)-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'	C [auth E], F [auth H]	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	I [auth C], J [auth F], K [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.295 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.238 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.569	α = 90
b = 106.16	β = 90
c = 125.329	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Nandakumar, J., Lima, C.D.

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description