3TY9 | pdb_00003ty9

Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate

PDB DOI: https://doi.org/10.2210/pdb3TY9/pdb

Classification: TRANSFERASE
Organism(s): Acetivibrio thermocellus ATCC 27405
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-09-24 Released: 2012-01-25
Deposition Author(s): Smith, P., Wang, L., Shuman, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free:
0.266 (Depositor), 0.260 (DCC)
R-Value Work:
0.219 (Depositor), 0.210 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.

Smith, P., Wang, L.K., Nair, P.A., Shuman, S.

(2012) Proc Natl Acad Sci U S A 109: 2296-2301

PubMed: 22308407 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1116827109
Primary Citation of Related Structures:
3TY5, 3TY8, 3TY9

PubMed Abstract:
Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase • ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique α-helical insert module and a unique C-terminal α-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.

Organizational Affiliation

Molecular Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.

Macromolecule Content

Total Structure Weight: 183.87 kDa
Atom Count: 12,300
Modelled Residue Count: 1,500
Deposited Residue Count: 1,572
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase	A, B, C, D	393	Acetivibrio thermocellus ATCC 27405	Mutation(s): 0 Gene Names: Cthe_2768 EC: 6.5.1.3
UniProt
Find proteins for A3DJ38 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DJ38 Go to UniProtKB: A3DJ38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DJ38
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	E [auth A], M [auth B], S [auth C], X [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	BA [auth D] I [auth A] J [auth A] O [auth B] P [auth B] BA [auth D], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] N [auth B] AA [auth D], F [auth A], G [auth A], H [auth A], N [auth B], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	CA [auth D], L [auth A], R [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain L [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain L [auth A] Focus chain R [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free: 0.266 (Depositor), 0.260 (DCC)
R-Value Work: 0.219 (Depositor), 0.210 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.5	α = 90
b = 132.76	β = 90
c = 162.77	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Smith, P.

Wang, L.

Shuman, S.

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2012-02-22
Changes: Database references
Version 1.2: 2012-02-29
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary