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- PDB-8yt1: Crystal structure of ACMSD in complex with malonate -

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Basic information

Entry
Database: PDB / ID: 8yt1
TitleCrystal structure of ACMSD in complex with malonate
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / kynurenine / decarboxylase / NAD homeostasis / tryptophan metabolism / metalloenzyme
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
MALONIC ACID / 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsYang, Y. / Liu, A.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA270879 United States
Welch FoundationAX-2110-20220331 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG078775 United States
National Science Foundation (NSF, China)32101016 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: alpha-Amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase catalyzes enol/keto tautomerization of oxaloacetate.
Authors: Yang, Y. / Davis, I. / Altman, R.A. / Liu, A.
History
DepositionMar 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4527
Polymers119,1523
Non-polymers3004
Water4,161231
1
A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules

A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7746
Polymers79,4352
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5780 Å2
ΔGint-128 kcal/mol
Surface area24050 Å2
MethodPISA
2
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
C: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5654
Polymers79,4352
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-109 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.278, 152.024, 153.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-37-

LYS

21A-531-

HOH

31A-599-

HOH

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Components

#1: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase / Alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase / ACMSD


Mass: 39717.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83V25
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: evaporation
Details: 2% (v/v) malonate pH 7.0, 0.1M sodium citrate tribasic pH 5.6, 12% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 59722 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.053 / Rrim(I) all: 0.135 / Χ2: 1.018 / Net I/σ(I): 5.9 / Num. measured all: 394895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.21-2.296.60.97259690.8110.9460.4061.0550.88599.8
2.29-2.386.30.72359300.8920.9710.3110.7880.91199.6
2.38-2.496.30.54258830.9110.9770.2330.5920.94898.6
2.49-2.6270.39760110.9550.9880.160.4290.93100
2.62-2.7870.28459810.9710.9930.1150.3070.96599.8
2.78-36.90.21359520.9810.9950.0870.230.9999.9
3-3.36.70.14560310.9860.9960.0610.1581.04199.8
3.3-3.786.30.1159790.9860.9970.0480.1211.17298.6
3.78-4.766.60.09258750.9870.9970.040.1011.09796.7
4.76-506.30.09661110.9910.9980.040.1041.26197.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→44.05 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1999 3.35 %
Rwork0.2079 --
obs0.2097 59670 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7743 0 10 231 7984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087955
X-RAY DIFFRACTIONf_angle_d0.90510780
X-RAY DIFFRACTIONf_dihedral_angle_d18.6682904
X-RAY DIFFRACTIONf_chiral_restr0.0521144
X-RAY DIFFRACTIONf_plane_restr0.0061420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.43351330.33243850X-RAY DIFFRACTION93
2.28-2.340.33421430.29674118X-RAY DIFFRACTION100
2.34-2.410.33541420.27784105X-RAY DIFFRACTION99
2.41-2.480.31761410.26274094X-RAY DIFFRACTION98
2.48-2.570.33041440.24374137X-RAY DIFFRACTION100
2.57-2.670.31011440.24394148X-RAY DIFFRACTION100
2.67-2.80.3261440.23834156X-RAY DIFFRACTION100
2.8-2.940.29231440.23954144X-RAY DIFFRACTION100
2.94-3.130.31521440.24624141X-RAY DIFFRACTION100
3.13-3.370.26341440.22414181X-RAY DIFFRACTION100
3.37-3.710.27381440.20264129X-RAY DIFFRACTION98
3.71-4.240.23381430.19054135X-RAY DIFFRACTION98
4.25-5.350.21031410.17384072X-RAY DIFFRACTION96
5.35-44.050.20971480.17134261X-RAY DIFFRACTION97

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