4U3E | pdb_00004u3e

Anaerobic ribonucleotide reductase

PDB DOI: https://doi.org/10.2210/pdb4U3E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-20 Released: 2014-09-03
Deposition Author(s): Funk, M.A., Drennan, C.L.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), ASTAR

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.200 (Depositor), 0.216 (DCC)
R-Value Work:
0.171 (Depositor), 0.189 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant.

Wei, Y., Funk, M.A., Rosado, L.A., Baek, J., Drennan, C.L., Stubbe, J.

(2014) Proc Natl Acad Sci U S A 111: E3756-E3765

PubMed: 25157154 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1414396111
Primary Citation Related Structures:
4U3E

PubMed Abstract:
The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO2. Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism.

Organizational Affiliation

Departments of Chemistry and yifwei@mit.edu cdrennan@mit.edu stubbe@mit.edu.

Macromolecule Content

Total Structure Weight: 158.44 kDa
Atom Count: 11,270
Modeled Residue Count: 1,256
Deposited Residue Count: 1,342
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside triphosphate reductase	A, B	671	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_0385, THEMA_02795, Tmari_0383 EC: 1.17.4.2
UniProt
Find proteins for Q9WYL6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYL6 Go to UniProtKB: Q9WYL6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

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: 1.64 Å
R-Value Free: 0.200 (Depositor), 0.216 (DCC)
R-Value Work: 0.171 (Depositor), 0.189 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.313	α = 90
b = 98.768	β = 111.72
c = 86.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Funk, M.A.

Drennan, C.L.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	0645960
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM29595
ASTAR	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2014-09-03
Type: Initial release
Version 1.1: 2014-10-01
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
Version 1.3: 2019-11-27
Changes: Author supporting evidence
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary