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- PDB-21gt: DPR epimerase complex, substrate-bound state -

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Basic information

Entry
Database: PDB / ID: 21gt
TitleDPR epimerase complex, substrate-bound state
Components(Decaprenylphosphoryl- ...) x 2
KeywordsISOMERASE / Epimerase complex / OXIDOREDUCTASE
Function / homology
Function and homology information


decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase / arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity ...decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase / arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / short chain dehydrogenase ...D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsWu, F. / Gao, S. / Rao, Z. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32394011 China
CitationJournal: To Be Published
Title: DPR epimerase complex, substrate-bound state
Authors: Wu, F. / Gao, S. / Rao, Z. / Zhang, L.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Decaprenylphosphoryl-beta-D-ribose oxidase
D: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase
A: Decaprenylphosphoryl-beta-D-ribose oxidase
C: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,96210
Polymers155,3274
Non-polymers3,6356
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Decaprenylphosphoryl- ... , 2 types, 4 molecules BADC

#1: Protein Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'- ...Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1 / Decaprenyl-phosphoribose 2'-epimerase subunit 1 / Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase / Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit / FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase


Mass: 50161.875 Da / Num. of mol.: 2 / Mutation: K418A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dprE1, Rv3790
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WJF1, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase
#2: Protein Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase / Decaprenyl-phospho-2'-keto-D-arabinose reductase / Decaprenylphospho-beta-D-erythro-pentofuranosid- ...Decaprenyl-phospho-2'-keto-D-arabinose reductase / Decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase / Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE2 / Decaprenyl-phosphoribose 2'-epimerase subunit 2 / NAD-dependent decaprenylphosphoryl-D-2-keto-erythropentose reductase


Mass: 27501.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: dprE2, Rv3791, MTCY13D12.25
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WGS9, decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-A1L5J / [(2~{E})-3,7-dimethylocta-2,6-dienyl] [(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate


Mass: 366.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DPR epimerase complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.155 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5 / Details: 150mM NaCl, 20mM Hepes
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312548 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 2.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0085668
ELECTRON MICROSCOPYf_angle_d1.27715
ELECTRON MICROSCOPYf_dihedral_angle_d7.478799
ELECTRON MICROSCOPYf_chiral_restr0.044863
ELECTRON MICROSCOPYf_plane_restr0.006988

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