4D05 | pdb_00004d05

Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium

PDB DOI: https://doi.org/10.2210/pdb4D05/pdb

Classification: LIGASE
Organism(s): Psychromonas sp. SP041
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-04-24 Released: 2014-11-12
Deposition Author(s): Williamson, A., Rothweiler, U., Leiros, H.-K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.192 (Depositor), 0.194 (DCC)
R-Value Work:
0.145 (Depositor), 0.148 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Enzyme-Adenylate Structure of a Bacterial ATP-Dependent DNA Ligase with a Minimized DNA-Binding Surface

Williamson, A., Rothweiler, U., Leiros, H.-K.S.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3043

PubMed: 25372693 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1399004714021099
Primary Citation Related Structures:
4D05

PubMed Abstract:
DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.

Organizational Affiliation

Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.

Macromolecule Content

Total Structure Weight: 61.19 kDa
Atom Count: 4,909
Modeled Residue Count: 507
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-DEPENDENT DNA LIGASE	A, B	258	Psychromonas sp. SP041	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAT9 (Psychromonas sp. SP041) Explore A0ACD6BAT9 Go to UniProtKB: A0ACD6BAT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
SO4 Query on SO4 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 F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.192 (Depositor), 0.194 (DCC)
R-Value Work: 0.145 (Depositor), 0.148 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.427	α = 90
b = 43.976	β = 105.92
c = 89.633	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Williamson, A.

Rothweiler, U.

Leiros, H.-K.S.

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2014-11-19
Changes: Database references
Version 2.0: 2017-06-28
Changes: Atomic model, Refinement description
Version 2.1: 2019-06-26
Changes: Data collection, Database references, Derived calculations, Experimental preparation, Structure summary
Version 2.2: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary