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- PDB-9q1a: Open state of lysine 5,6-aminomutase from Thermoanaerobacter teng... -

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Basic information

Entry
Database: PDB / ID: 9q1a
TitleOpen state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Components
  • D-lysine 5,6-aminomutase alpha subunit
  • D-lysine 5,6-aminomutase beta subunit
KeywordsISOMERASE / lysine 5 / 6-aminomutase / cobalamin / vitamin B12 / pyridoxal phosphate / radical
Function / homology
Function and homology information


cobalamin binding / catalytic activity / protein dimerization activity / metal ion binding
Similarity search - Function
D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily / D-Lysine 5,6-aminomutase alpha subunit superfamily / D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit / Dimerisation domain of d-ornithine 4,5-aminomutase / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / D-lysine 5,6-aminomutase beta subunit / D-lysine 5,6-aminomutase alpha subunit
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsTian, S. / Tjia-Fleck, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM155016 United States
CitationJournal: To Be Published
Title: Catalysis in Motion: Large-Scale Domain Alternation Enables Co(III)-C Bond Homolysis in Lysine 5,6-Aminomutase
Authors: Tian, S. / Tjia-Fleck, S.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
SupersessionSep 10, 2025ID: 8T0Q
Revision 1.1Sep 10, 2025Group: Advisory / Data collection
Category: em_admin / em_obsolete / pdbx_database_PDB_obs_spr
Item: _em_admin.last_update
Revision 1.1Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Advisory / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata
Category: em_admin / em_obsolete / pdbx_database_PDB_obs_spr
Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-lysine 5,6-aminomutase beta subunit
B: D-lysine 5,6-aminomutase beta subunit
C: D-lysine 5,6-aminomutase alpha subunit
D: D-lysine 5,6-aminomutase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,2768
Polymers173,1134
Non-polymers3,1634
Water00
1


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

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Components

#1: Protein D-lysine 5,6-aminomutase beta subunit


Mass: 28612.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: TTE0727 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBT2
#2: Protein D-lysine 5,6-aminomutase alpha subunit


Mass: 57943.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: TTE0726 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBT3
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 57.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1482472 / Symmetry type: POINT

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