4HFQ | pdb_00004hfq

Crystal structure of UDP-X diphosphatase

PDB DOI: https://doi.org/10.2210/pdb4HFQ/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-05 Released: 2013-08-07
Deposition Author(s): Duong-Ly, K.C., Amzel, L.M., Gabelli, S.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.196 (Depositor), 0.195 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis.

Duong-Ly, K.C., Woo, H.N., Dunn, C.A., Xu, W., Babic, A., Bessman, M.J., Amzel, L.M., Gabelli, S.B.

(2013) PLoS One 8: e64241-e64241

PubMed: 23691178 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0064241
Primary Citation Related Structures:
4HFQ

PubMed Abstract:
The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 Å resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3'5' RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.

Organizational Affiliation

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

Macromolecule Content

Total Structure Weight: 49.64 kDa
Atom Count: 4,205
Modeled Residue Count: 406
Deposited Residue Count: 406
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/nudix family protein	A, B	203	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: SP1669, SP_1669
UniProt
Find proteins for A0A0H2URA0 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URA0 Go to UniProtKB: A0A0H2URA0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2URA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain E [auth A]	E [auth A], X [auth B], Z [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain X [auth B] Focus chain Z [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain FA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth B]	FA [auth B], I [auth A], L [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain I [auth A] Focus chain L [auth A] Focus chain R [auth A] Interactions & Density Focus chain FA [auth B] Focus chain I [auth A] Focus chain L [auth A] Focus chain R [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain M [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], M [auth A], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth A] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain K [auth A] SDF format, chain AA [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth B]	AA [auth B] K [auth A] P [auth A] Q [auth A] V [auth B] AA [auth B], K [auth A], P [auth A], Q [auth A], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth B] Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain U [auth B] SDF format, chain S [auth A] SDF format, chain N [auth A] SDF format, chain J [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] SDF format, chain C [auth A] SDF format, chain BA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] MOL2 format, chain N [auth A] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A] mmCIF format, chain N [auth A] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth B]	BA [auth B] C [auth A] CA [auth B] D [auth A] DA [auth B] BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], EA [auth B], J [auth A], N [auth A], S [auth A], U [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain J [auth A] Focus chain N [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain J [auth A] Focus chain N [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain Y [auth B]