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Open data
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Basic information
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Title | Cryo-EM structure of FtAlkB | |||||||||
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Function / homology | Alkane/xylene monooxygenase / Fatty acid desaturase domain / Fatty acid desaturase / monooxygenase activity / lipid metabolic process / plasma membrane / Alkane 1-monooxygenase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
![]() | Zhang J / Feng L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and mechanism of the alkane-oxidizing enzyme AlkB. Authors: Xue Guo / Jianxiu Zhang / Lei Han / Juliet Lee / Shoshana C Williams / Allison Forsberg / Yan Xu / Rachel Narehood Austin / Liang Feng / ![]() Abstract: Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase ...Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 22.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.4 KB | Display | ![]() |
Images | ![]() | 134.3 KB | ||
Masks | ![]() | 42.9 MB | ![]() | |
Others | ![]() ![]() ![]() | 37.9 MB 39.8 MB 39.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sbbMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : FtAklB-Nanobody
Entire | Name: FtAklB-Nanobody |
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Components |
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-Supramolecule #1: FtAklB-Nanobody
Supramolecule | Name: FtAklB-Nanobody / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Alkane 1-monooxygenase
Macromolecule | Name: Alkane 1-monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.56948 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MATSMGSHPG FGADSSGTIA YRDRKRPFWT LSVLWPVSPL IGIYLAHTTG VGAFFWLTLA VWYLIIPLLD WVLGDDQSNP PEAVVPALE SDRYYRILTY LTVPIHYVVL IGSAWYVSTH YGSMTWYDIL GLALSVGIVN GLAINTGHEL GHKKTELERW L AKIVLAVV ...String: MATSMGSHPG FGADSSGTIA YRDRKRPFWT LSVLWPVSPL IGIYLAHTTG VGAFFWLTLA VWYLIIPLLD WVLGDDQSNP PEAVVPALE SDRYYRILTY LTVPIHYVVL IGSAWYVSTH YGSMTWYDIL GLALSVGIVN GLAINTGHEL GHKKTELERW L AKIVLAVV GYGHFFIEHN KGHHKDVATP EDPASAPFGQ SIYRFALREI PGAIIRAWNS EKERLGRLGH SPWSLQNEVL QP LLITIPL YVGLIAVLGV KIIPFLLIQI VFGWWQLTSA NYIEHYGLLR QKLPDGRYER CQPYHSWNSN HVMSNLILFH LQR HSDHHA HPTRRYQSLR DFPDLPTLPS GYPLMFALSY FPPLWRAVMD RRVLDVCGRD ARKINIDPNQ REKIIHKFNL LTG |
-Macromolecule #2: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.502039 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAQVQLQESG GGLVQAGGSL RLSCAASGTI SRYWTMGWYR QAPGKERELV AGISEGGSTN YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV TYRGPWFNRD PHYYWGQGTQ VTVSSHHHHH H |
-Macromolecule #3: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #4: DODECANE
Macromolecule | Name: DODECANE / type: ligand / ID: 4 / Number of copies: 1 / Formula: D12 |
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Molecular weight | Theoretical: 170.335 Da |
Chemical component information | ![]() ChemComp-D12: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |