SASDFM5: Mutant 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, H1...

Basic information

• Entry: Database: SASBDB / ID: SASDFM5

Sample

Mutant 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, H110A tetramer, at pH 8.5

• 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase (protein), ACMSD, Pseudomonas fluorescens

Function / homology

Function:

secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol

Domain/homology:

2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase

Component:

2-amino-3-carboxymuconate 6-semialdehyde decarboxylase

• 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 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

• Yu Yang (University of Texas at San Antonio, San Antonia, TX, USA)

Models

• Model #2961: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.250 / P-value: 0.063313; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Mutant 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, H110A tetramer, at pH 8.5
• Buffer: Name: 50 mM Tris, 5 mM DTT / pH: 8.5

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 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: 0.1228 Å / Dist. spec. to detc.: 2.5 mm
• Detector: Name: Pilatus3 X 1M / Pixsize x: 0.172 mm

Scan

Title: Mutant 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase, H110A tetramer, at pH 8.5
Measurement date: Jul 15, 2018 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 1 sec. / Number of frames: 500 / Unit: 1/A /

	Min	Max
Q	0.014	0.3003

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 409 /

	Min	Max
Q	0.00654362	0.145407
P(R) point	1	409
R	0	190

Result

Type of curve: sec /

	Experimental	Porod
MW	158.8 kDa	148.8 kDa
Volume	-	238 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	13.77	0.19	13.309	0.376
Radius of gyration, Rg	5.6 nm	0.08	5.22 nm	0.195

	Min	Max
D	-	19
Guinier point	1	31