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- EMDB-72121: Open state of lysine 5,6-aminomutase from Thermoanaerobacter teng... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72121
TitleOpen state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Map data
Sample
  • Complex: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
    • Protein or peptide: D-lysine 5,6-aminomutase beta subunit
    • Protein or peptide: D-lysine 5,6-aminomutase alpha subunit
  • Ligand: COBALAMIN
  • Ligand: 5'-DEOXYADENOSINE
Keywordslysine 5 / 6-aminomutase / cobalamin / vitamin B12 / pyridoxal phosphate / radical / ISOMERASE
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
D-lysine 5,6-aminomutase beta subunit / D-lysine 5,6-aminomutase alpha subunit
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsTian S / Tjia-Fleck S
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
SupersessionSep 10, 2025ID: EMD-40945
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72121.png

Downloads & links

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Map

FileDownload / File: emd_72121.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0474
Minimum - Maximum-0.10224766 - 0.31839758
Average (Standard dev.)0.00013040093 (±0.006203768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72121_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72121_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

EntireName: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Components
  • Complex: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
    • Protein or peptide: D-lysine 5,6-aminomutase beta subunit
    • Protein or peptide: D-lysine 5,6-aminomutase alpha subunit
  • Ligand: COBALAMIN
  • Ligand: 5'-DEOXYADENOSINE

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Supramolecule #1: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

SupramoleculeName: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

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

MacromoleculeName: D-lysine 5,6-aminomutase beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 28.612801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QYDTTLDLTR VKPYGDTMND GKVQLSFTLP VPDGAKAVEA AKQLAKKMGL ENPMVVYHAP LDKNFTFFII YGSLIHTVDY TSIQVQELE IKAMSMEETN EYIKKHIGRK VVVVGATTGT DAHTVGLDAI MNM(LLP)GYAGHY GLERYEMIEA YNLGSQV PN EEFVKKAIEV ...String:
QYDTTLDLTR VKPYGDTMND GKVQLSFTLP VPDGAKAVEA AKQLAKKMGL ENPMVVYHAP LDKNFTFFII YGSLIHTVDY TSIQVQELE IKAMSMEETN EYIKKHIGRK VVVVGATTGT DAHTVGLDAI MNM(LLP)GYAGHY GLERYEMIEA YNLGSQV PN EEFVKKAIEV GADALLVSQT VTQKDAHIKN LTHLVELLEA EGIRDKVLLI CGGPRITHEL AKELGYDAGF GPGTFADH V ATFIVTEMVK RKIPGLKGYK

UniProtKB: D-lysine 5,6-aminomutase beta subunit

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Macromolecule #2: D-lysine 5,6-aminomutase alpha subunit

MacromoleculeName: D-lysine 5,6-aminomutase alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 57.943477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RESKLNLDWE LVDKAREAAR NIVKDTQKFI DAHTTVSVER TVCRLLGIDG VNDLGVPLPN VVVDHIKSKG NLSLGAATYI GNAMIYTGL SPQEIAERVA KGELDLTSIP MADLFEIKLA VQDIAIKTVE KIRENRRKRE EFLKKYGDKE GPLLYVIVAT G NIYEDVVQ ...String:
RESKLNLDWE LVDKAREAAR NIVKDTQKFI DAHTTVSVER TVCRLLGIDG VNDLGVPLPN VVVDHIKSKG NLSLGAATYI GNAMIYTGL SPQEIAERVA KGELDLTSIP MADLFEIKLA VQDIAIKTVE KIRENRRKRE EFLKKYGDKE GPLLYVIVAT G NIYEDVVQ AQAAARQGAD VIAVIRATAQ SLLDYVPYGP TTEGFGGTYA TQENFRIMRK ALDEVSEELG RYIRLCNYAS GL CMPEIAA MGALERLDVM LNDALYGILF RDINMKRTMV DQFFSRVING FAGIIINTGE DNYLTTADAY EKAHTVLASQ LIN EQFALI AGIPEEQMGL GHAFEMNPDL RNGFLYELAQ AQMVREIFPK APLKYMPPTK YMTGNIFKGH VQDAMFNVVT IMTK QRIHL LGMLTEAIHT PFMSDRALSI ESAKYIFNNM ADIADEIYFK EGGIIQRRAN EVLKKAYELL KEIEQEGLFK ALEQG KFAD IKRPIDGGKG LEGVVEKDPN YFNPFIDLML RGD

UniProtKB: D-lysine 5,6-aminomutase alpha subunit

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Macromolecule #3: COBALAMIN

MacromoleculeName: COBALAMIN / type: ligand / ID: 3 / Number of copies: 2 / Formula: B12
Molecular weightTheoretical: 1.330356 KDa
Chemical component information

ChemComp-B12:
COBALAMIN

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Macromolecule #4: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 57.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1482472
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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