Macromolecule Content

Total Structure Weight: 472.08 kDa
Atom Count: 31,256
Modelled Residue Count: 3,629
Deposited Residue Count: 3,970
Unique protein chains: 1

3MJ4

Crystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose

PDB DOI: https://doi.org/10.2210/pdb3MJ4/pdb

Classification: ISOMERASE
Organism(s): Deinococcus radiodurans R1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-12 Released: 2010-10-20
Deposition Author(s): Karunan Partha, S., Sadeghi-Khomami, A., Slowski, K., Kotake, T., Thomas, N.R., Jakeman, D.L., Sanders, D.A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.262
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase.

Partha, S.K., Sadeghi-Khomami, A., Slowski, K., Kotake, T., Thomas, N.R., Jakeman, D.L., Sanders, D.A.

(2010) J Mol Biol 403: 578-590

PubMed: 20850454 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2010.08.053
Primary Citation of Related Structures:
3MJ4

PubMed Abstract:

UDP (uridine diphosphate) galactopyranose mutase (UGM) is involved in the cell wall biosynthesis of many pathogenic microorganisms. UGM catalyzes the reversible conversion of UDP-α-D-galactopyranose into UDP-α-D-galactofuranose, with the latter being the precursor of galactofuranose (Galf) residues in cell walls. Glycoconjugates of Galf are essential components in the cell wall of various pathogenic bacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis. The absence of Galf in humans and its bacterial requirement make UGM a potential target for developing novel antibacterial agents. In this article, we report the synthesis, inhibitory activity, and X-ray crystallographic studies of UDP-phosphono-galactopyranose, a nonhydrolyzable C-glycosidic phosphonate. This is the first report on the synthesis of a phosphonate analog of UDP-α-D-galactopyranose by a chemoenzymatic phosphoryl coupling method. The phosphonate was evaluated against three bacterial UGMs and showed only moderate inhibition. We determined the crystal structure of the phosphonate analog bound to Deinococcus radiodurans UGM at 2.6 Å resolution. The phosphonate analog is bound in a novel conformation not observed in UGM-substrate complex structures or in other enzyme-sugar nucleotide phosphonate complexes. This complex structure provides a structural basis for the observed micromolar inhibition towards UGM. Steric clashes, loss of electrostatic stabilization between an active-site arginine (Arg305) and the phosphonate analog, and a 180° flip of the hexose moiety account for the differences in the binding orientations of the isosteric phosphonate analog and the physiological substrate. This provides new insight into the ability of a sugar-nucleotide-binding enzyme to orient a substrate analog in an unexpected geometry and should be taken into consideration in designing such enzyme inhibitors.

Organizational Affiliation:

Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B, C, D, E, F, G, H, I, J A, B, C, D, E, F, G, H, I, J	397	Deinococcus radiodurans R1	Mutation(s): 0 Gene Names: DR_A0367, DR_AO367 EC: 5.4.99.9
UniProt
Find proteins for Q9RYF1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Explore Q9RYF1 Go to UniProtKB: Q9RYF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RYF1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BB [auth J] SDF format, chain GA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain S [auth C] SDF format, chain UA [auth I] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BB [auth J] MOL2 format, chain GA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain UA [auth I] MOL2 format, chain X [auth D]	AA [auth E], BB [auth J], GA [auth F], K [auth A], LA [auth G], AA [auth E], BB [auth J], GA [auth F], K [auth A], LA [auth G], P [auth B], QA [auth H], S [auth C], UA [auth I], X [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
URM Query on URM Download Ideal Coordinates CCD File SDF format, chain W [auth D] MOL2 format, chain W [auth D]	W [auth D]	(((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride C₁₆ H₂₆ N₂ O₁₆ P₂ WUPLBUVQIJIOHV-PPSAJGQHSA-N		Ligand Interaction
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CB [auth J] SDF format, chain HA [auth F] SDF format, chain L [auth A] SDF format, chain MA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain T [auth C] SDF format, chain WA [auth I] MOL2 format, chain BA [auth E] MOL2 format, chain CB [auth J] MOL2 format, chain HA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain WA [auth I]	BA [auth E], CB [auth J], HA [auth F], L [auth A], MA [auth G], BA [auth E], CB [auth J], HA [auth F], L [auth A], MA [auth G], Q [auth B], RA [auth H], T [auth C], WA [auth I]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Ligand Interaction
XYL Query on XYL Download Ideal Coordinates CCD File SDF format, chain JA [auth F] SDF format, chain VA [auth I] MOL2 format, chain JA [auth F] MOL2 format, chain VA [auth I]	JA [auth F], VA [auth I]	Xylitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-SCDXWVJYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain DB [auth J] SDF format, chain EA [auth E] SDF format, chain EB [auth J] SDF format, chain FA [auth E] SDF format, chain IA [auth F] SDF format, chain KA [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain R [auth B] SDF format, chain SA [auth H] SDF format, chain TA [auth H] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain XA [auth I] SDF format, chain Y [auth D] SDF format, chain YA [auth I] SDF format, chain Z [auth D] SDF format, chain ZA [auth I] MOL2 format, chain AB [auth I] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth J] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth J] MOL2 format, chain FA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain XA [auth I] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth I] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth I]	AB [auth I], CA [auth E], DA [auth E], DB [auth J], EA [auth E], AB [auth I], CA [auth E], DA [auth E], DB [auth J], EA [auth E], EB [auth J], FA [auth E], IA [auth F], KA [auth F], M [auth A], N [auth A], NA [auth G], O [auth A], OA [auth G], PA [auth G], R [auth B], SA [auth H], TA [auth H], U [auth C], V [auth C], XA [auth I], Y [auth D], YA [auth I], Z [auth D], ZA [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.262
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.149	α = 90
b = 175.715	β = 90
c = 223.99	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
MxDC	data collection
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary