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Yorodumi- SASDFN5: Wild type 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase,... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDFN5 |
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Sample | Wild type 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, ACMSD tetramer, at pH 7.0
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Function / homology | Function and homology information secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function |
Biological species | Pseudomonas fluorescens (bacteria) |
Citation | Journal: J Biol Chem / Year: 2019 Title: Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity. Authors: Yu Yang / Ian Davis / Tsutomu Matsui / Ivan Rubalcava / Aimin Liu / Abstract: α-Amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) plays an important role in l-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive ...α-Amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) plays an important role in l-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive as a monomer because its catalytic assembly requires an arginine residue from a neighboring subunit. However, how the oligomeric state and self-association of ACMSD are controlled in solution remains unexplored. Here, we demonstrate that ACMSD from can self-assemble into homodimer, tetramer, and higher-order structures. Using size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis, we investigated the ACMSD tetramer structure, and fitting the SAXS data with X-ray crystal structures of the monomeric component, we could generate a pseudo-atomic structure of the tetramer. This analysis revealed a tetramer model of ACMSD as a head-on dimer of dimers. We observed that the tetramer is catalytically more active than the dimer and is in equilibrium with the monomer and dimer. Substituting a critical residue of the dimer-dimer interface, His-110, altered the tetramer dissociation profile by increasing the higher-order oligomer portion in solution without changing the X-ray crystal structure. ACMSD self-association was affected by pH, ionic strength, and other electrostatic interactions. Alignment of ACMSD sequences revealed that His-110 is highly conserved in a few bacteria that utilize nitrobenzoic acid as a sole source of carbon and energy, suggesting a dedicated functional role of ACMSD's self-assembly into the tetrameric and higher-order structures. These results indicate that the dynamic oligomerization status potentially regulates ACMSD activity and that SEC-SAXS coupled with X-ray crystallography is a powerful tool for studying protein self-association. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDFN5 |
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-Related structure data
-External links
Related items in Molecule of the Month |
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-Models
Model #2959 | Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.25 / P-value: 0.015811 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: Wild type 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, ACMSD tetramer, at pH 7.0 |
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Buffer | Name: 25 mM HEPES, 5 mM DTT / pH: 7 |
Entity #1627 | Name: ACMSD / Type: protein Description: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase Formula weight: 39.661 / Num. of mol.: 4 / Source: Pseudomonas fluorescens / References: UniProt: Q83V25 Sequence: MGHHHHHHHH HHSSGHIEGR HMKKPRIDMH SHFFPRISEQ EAAKFDANHA PWLQVSAKGD TGSIMMGKNN FRPVYQALWD PAFRIEEMDA QGVDVQVTCA TPVMFGYTWE ANKAAQWAER MNDFALEFAA HNPQRIKVLA QVPLQDLDLA CKEASRAVAA GHLGIQIGNH ...Sequence: MGHHHHHHHH HHSSGHIEGR HMKKPRIDMH SHFFPRISEQ EAAKFDANHA PWLQVSAKGD TGSIMMGKNN FRPVYQALWD PAFRIEEMDA QGVDVQVTCA TPVMFGYTWE ANKAAQWAER MNDFALEFAA HNPQRIKVLA QVPLQDLDLA CKEASRAVAA GHLGIQIGNH LGDKDLDDAT LEAFLTHCAN EDIPILVHPW DMMGGQRMKK WMLPWLVAMP AETQLAILSL ILSGAFERIP KSLKICFGHG GGSFAFLLGR VDNAWRHRDI VREDCPRPPS EYVDRFFVDS AVFNPGALEL LVSVMGEDRV MLGSDYPFPL GEQKIGGLVL SSNLGESAKD KIISGNASKF FNINV |
-Experimental information
Beam | Instrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2 City: Menlo Park, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1088 Å / Dist. spec. to detc.: 1.7 mm | |||||||||||||||||||||||||||||||||
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Detector | Name: Pilatus3 X 1M / Pixsize x: 0.172 mm | |||||||||||||||||||||||||||||||||
Scan | Title: Wild type 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, ACMSD tetramer, at pH 7.0 Measurement date: Jan 10, 2018 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 1 sec. / Number of frames: 500 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 306 /
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Result | Type of curve: sec /
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