+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39390 | |||||||||
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Title | The structure of DSR2 and NAD+ complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / IMMUNE SYSTEM | |||||||||
Function / homology | SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein Function and homology information | |||||||||
Biological species | Bacillus subtilis subsp. natto (strain BEST195) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Zheng J / Yang X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Int J Biol Macromol / Year: 2024 Title: Structural insights into autoinhibition and activation of defense-associated sirtuin protein. Authors: Xu Yang / Yiqun Wang / Jianting Zheng / Abstract: Bacterial defense-associated sirtuin 2 (DSR2) proteins harbor an N-terminal sirtuin (SIR2) domain degrading NAD. DSR2 from Bacillus subtilis 29R is autoinhibited and unable to hydrolyze NAD in the ...Bacterial defense-associated sirtuin 2 (DSR2) proteins harbor an N-terminal sirtuin (SIR2) domain degrading NAD. DSR2 from Bacillus subtilis 29R is autoinhibited and unable to hydrolyze NAD in the absence of phage infection. A tail tube protein (TTP) of phage SPR activates the DSR2 while a DSR2-inhibiting protein of phage SPbeta, known as DSAD1 (DSR anti-defense 1), inactivates the DSR2. Although DSR2 structures in complexed with TTP and DSAD1, respectively, have been reported recently, the autoinhibition and activation mechanisms remain incompletely understood. Here, we present cryo-electron microscopy structures of the DSR2-NAD complex in autoinhibited state and the in vitro assembled DSR2-TFD (TTP tube-forming domain) complex in activated state. The DSR2-NAD complex reveals that the autoinhibited DSR2 assembles into an inactive tetramer, binding NAD through a distinct pocket situated outside active site. Binding of TFD into cavities within the sensor domains of DSR2 triggers a conformational change in SIR2 regions, activating its NADase activity, whereas the TTP β-sandwich domain (BSD) is flexible and does not contribute to the activation process. The activated form of DSR2 exists as tetramers and dimers, with the tetramers exhibiting more NADase activity. Overall, our results extend the current understanding of autoinhibition and activation of DSR2 immune proteins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39390.map.gz | 211.7 MB | EMDB map data format | |
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Header (meta data) | emd-39390-v30.xml emd-39390.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39390_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_39390.png | 81.5 KB | ||
Masks | emd_39390_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-39390.cif.gz | 6.3 KB | ||
Others | emd_39390_half_map_1.map.gz emd_39390_half_map_2.map.gz | 392.1 MB 392.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39390 | HTTPS FTP |
-Validation report
Summary document | emd_39390_validation.pdf.gz | 1010.2 KB | Display | EMDB validaton report |
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Full document | emd_39390_full_validation.pdf.gz | 1009.7 KB | Display | |
Data in XML | emd_39390_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | emd_39390_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39390 | HTTPS FTP |
-Related structure data
Related structure data | 8yltMC 8ykfC 8yl5C 8ylnC 8z18C 8ztrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39390.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_39390_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39390_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39390_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the complex of DSR2 with NAD
Entire | Name: the complex of DSR2 with NAD |
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Components |
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-Supramolecule #1: the complex of DSR2 with NAD
Supramolecule | Name: the complex of DSR2 with NAD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria) |
-Macromolecule #1: SIR2-like domain-containing protein
Macromolecule | Name: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria) |
Molecular weight | Theoretical: 118.635789 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL ...String: MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL KVHGDFRKGF KGENVVLKED DYLNYDQNYP LISNLMKTII ATHTIVFIGY GLGDYNINML LNWVRKLQKD SF HKPFFIR TDPSPIENET LIYYENKGLR IIDAASLIDS NEYDYLERYS AVMDLLIESQ ENKFITKDDE VIDYIYGKIS PLF ALQYIR KIDLKHVFEY DYHFEVNGTV VRHKNKGFGY MERFFELKES CDERSKLSKK QYERFNALFN FFEKNGVICM AKDA GTLNT SIEINSLAYH GKYDVMKKFI EEQSVSIEDD YKKAFFLACL GRWEESYDLY SNIILNSIDE SNGCVYYLSQ INRYR IYQS ITQAVTQFNG LGLLTFGRHY KPFTDEFLAR IEREMTNFNI DDLFNGMPFE FQKKYKILEF LSDNQFLYDD TVKLFE LTN KVRSEMSEGS YSFGMSSDIV VLLRLYDNLR FLYENCLWSV SFHEFHQYIR NSMSLLIEKA EYERTRDIDE LGFSFFG KK SGFFMEYYDF VNISRHFKID DIKNLERSCS IDKIRFGEQE KIEEYLVGIA EEITKQFSAN GMNVVFYTQF ISEAKAAL Y FAKYVKLSEE GLGKIVKALL FYFPERDLDI GKRYVWLERL TKCNELPKSI ISIIDDFLVL QAEKHIDQNY SEVSSNGLY SRDYGALIKH FEKNFISKRL SEITLCLTQD KQKQIDFLFK LLPLLSTNAK SHLLSFKSVE NINDLMNGIR IGLIDEFTPE HEELIIEYL ETRKVNYIVE KEKGIQTFSS NDYMSTFGIW YFLEEINNSK MEEFIGMDDQ YDFFVDPENF DYKKFIPSWL K NYNDKLLG KIAGNKHMKH HVIEVLKERV KNSNDKRYLE ILMNYFI UniProtKB: SIR2-like domain-containing protein |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |