4HX9 | pdb_00004hx9

Designed Phosphodeoxyribosyltransferase

PDB DOI: https://doi.org/10.2210/pdb4HX9/pdb

Classification: TRANSFERASE
Organism(s): Lactobacillus leichmannii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-11-09 Released: 2013-01-16
Deposition Author(s): Kaminski, P.A., Labesse, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.250 (Depositor), 0.242 (DCC)
R-Value Work:
0.195 (Depositor), 0.192 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.

Kaminski, P.A., Labesse, G.

(2013) J Biological Chem 288: 6534-6541

PubMed: 23325804 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.446492
Primary Citation Related Structures:
4HX9

PubMed Abstract:
A large number of nucleoside analogues and 2'-deoxynucleoside triphosphates (dNTP) have been synthesized to interfere with DNA metabolism. However, in vivo the concentration and phosphorylation of these analogues are key limiting factors. In this context, we designed enzymes to switch nucleobases attached to a deoxyribose monophosphate. Active chimeras were made from two distantly related enzymes: a nucleoside deoxyribosyltransferase from lactobacilli and a 5'-monophosphate-2'-deoxyribonucleoside hydrolase from rat. Then their unprecedented activity was further extended to deoxyribose triphosphate, and in vitro biosyntheses could be successfully performed with several base analogues. These new enzymes provide new tools to synthesize dNTP analogues and to deliver them into cells.

Organizational Affiliation

Institut Pasteur, Unité de Chimie et Biocatalyse, CNRS, UMR 3523, 75724 Paris cedex 15, France. pierre-alexandre.kaminski@pasteur.fr

Macromolecule Content

Total Structure Weight: 146.7 kDa
Atom Count: 10,448
Modeled Residue Count: 1,245
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A B C [auth E] D [auth F] E [auth C] A, B, C [auth E], D [auth F], E [auth C], F [auth D], G, H	157	Lactobacillus leichmannii	Mutation(s): 5 Gene Names: ntd EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii) Explore Q9R5V5 Go to UniProtKB: Q9R5V5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9R5V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	K [auth A] M [auth B] R [auth F] S [auth F] W [auth D] K [auth A], M [auth B], R [auth F], S [auth F], W [auth D], X [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth F] Focus chain S [auth F] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth F] Focus chain S [auth F] Focus chain W [auth D] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain BA [auth H] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	AA [auth H] BA [auth H] I [auth A] J [auth A] L [auth B] AA [auth H], BA [auth H], I [auth A], J [auth A], L [auth B], N [auth E], O [auth E], P [auth F], Q [auth F], T [auth C], U [auth D], V [auth D], Y [auth G], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.250 (Depositor), 0.242 (DCC)
R-Value Work: 0.195 (Depositor), 0.192 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.454	α = 90
b = 218.454	β = 90
c = 218.454	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Kaminski, P.A.

Labesse, G.

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2013-02-13
Changes: Database references
Version 1.2: 2013-03-20
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4HX9 | pdb_00004hx9

Designed Phosphodeoxyribosyltransferase

Literature

Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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