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- PDB-7pwy: Structure of human dimeric ACMSD in complex with the inhibitor TE... -

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Basic information

Entry
Database: PDB / ID: 7pwy
TitleStructure of human dimeric ACMSD in complex with the inhibitor TES-1025
Components2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
KeywordsLYASE / ACMSD / de-novo NAD+ synthesis / TES-1025 / decarboxylase
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding ...aminocarboxymuconate-semialdehyde decarboxylase / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-8EK / : / 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCianci, M. / Giacche, N. / Carotti, A. / Liscio, P. / Amici, A. / Cialabrini, L. / De Franco, F. / Pellicciari, R. / Raffaelli, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Basis of Human Dimeric alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase Inhibition With TES-1025.
Authors: Cianci, M. / Giacche, N. / Cialabrini, L. / Carotti, A. / Liscio, P. / Rosatelli, E. / De Franco, F. / Gasparrini, M. / Robertson, J. / Amici, A. / Raffaelli, N. / Pellicciari, R.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 2.0May 11, 2022Group: Database references / Non-polymer description / Category: chem_comp / citation
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
C: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
D: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,60016
Polymers152,3374
Non-polymers1,26312
Water5,206289
1
A: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,22310
Polymers76,1682
Non-polymers1,0548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
D: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3776
Polymers76,1682
Non-polymers2094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.410, 92.579, 103.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

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Components

#1: Protein
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Picolinate carboxylase / alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase


Mass: 38084.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACMSD / Production host: Komagataella pastoris (fungus)
References: UniProt: Q8TDX5, aminocarboxymuconate-semialdehyde decarboxylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8EK / 2-[3-[(5-cyano-6-oxidanylidene-4-thiophen-2-yl-1H-pyrimidin-2-yl)sulfanylmethyl]phenyl]ethanoic acid


Mass: 383.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 100 mM Na(CH3COO), 22% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.5→45.89 Å / Num. obs: 51945 / % possible obs: 99.9 % / Observed criterion σ(I): 1.6 / Redundancy: 7.6 % / Biso Wilson estimate: 52.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4423 / CC1/2: 0.766 / CC star: 0.926 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSVERSION Jun 1, 2017data reduction
Aimless0.5.32data scaling
PHASER1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IH3

4ih3


Resolution: 2.5→45.33 Å / SU ML: 0.3606 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 2565 4.97 %Random
Rwork0.2105 49045 --
obs0.2125 51610 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10248 0 62 289 10599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002510635
X-RAY DIFFRACTIONf_angle_d0.547414398
X-RAY DIFFRACTIONf_chiral_restr0.04281538
X-RAY DIFFRACTIONf_plane_restr0.00491835
X-RAY DIFFRACTIONf_dihedral_angle_d16.57583962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.35991560.32042652X-RAY DIFFRACTION99.57
2.55-2.60.36951630.29832687X-RAY DIFFRACTION99.79
2.6-2.660.32031270.2912708X-RAY DIFFRACTION99.86
2.66-2.720.38111240.2942742X-RAY DIFFRACTION99.9
2.72-2.790.31571440.26892693X-RAY DIFFRACTION99.89
2.79-2.860.32711300.26092699X-RAY DIFFRACTION99.79
2.86-2.950.30651370.26442718X-RAY DIFFRACTION99.62
2.95-3.040.28061430.26262714X-RAY DIFFRACTION99.76
3.04-3.150.28491420.2452725X-RAY DIFFRACTION99.69
3.15-3.280.28891310.22542716X-RAY DIFFRACTION99.72
3.28-3.420.24981510.22232714X-RAY DIFFRACTION99.72
3.42-3.610.28911540.23992706X-RAY DIFFRACTION99.72
3.61-3.830.28751160.252570X-RAY DIFFRACTION92.59
3.83-4.130.21661540.18562726X-RAY DIFFRACTION99.9
4.13-4.540.20971420.16282754X-RAY DIFFRACTION99.38
4.54-5.20.18221510.15862778X-RAY DIFFRACTION99.9
5.2-6.550.23651540.19372802X-RAY DIFFRACTION99.93
6.55-45.330.21821460.17312941X-RAY DIFFRACTION99.58

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