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- PDB-8fft: Structure of GntC, a PLP-dependent enzyme catalyzing L-enduracidi... -

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Basic information

Entry
Database: PDB / ID: 8fft
TitleStructure of GntC, a PLP-dependent enzyme catalyzing L-enduracididine biosynthesis from (S)-4-hydroxy-L-arginine
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsBIOSYNTHETIC PROTEIN / PLP / GntC / cyclodehydration / (S)-4-hydroxy-L-arginine / guanitoxin / L-enduracididine / cyanobacterial blooms / biocatalysis / biosynthesis / cyanobacterium
Function / homologytransaminase activity / biosynthetic process / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Function and homology information
Biological speciesDolichospermum flos-aquae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, P.Y.-T. / Lima, S.T. / Chekan, J.R. / Moore, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R21-ES032056 United States
Citation
Journal: Acs Catalysis / Year: 2023
Title: Mechanistic and Structural Insights into a Divergent PLP-Dependent l-Enduracididine Cyclase from a Toxic Cyanobacterium.
Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.K.
#1: Journal: Biorxiv / Year: 2023
Title: Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium.
Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.K.
History
DepositionDec 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,5849
Polymers167,4634
Non-polymers1225
Water1,856103
1
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8045
Polymers83,7312
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-45 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7804
Polymers83,7312
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-38 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.855, 158.159, 73.231
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme


Mass: 41865.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dolichospermum flos-aquae (bacteria) / Gene: K2F26_16465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8G0W655
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 19% (w/v) PEG 3350, 0.50 M MgCl2, 0.10 M Tris pH 8.5, and 1 mM PLP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99992 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.1→73.23 Å / Num. obs: 75093 / % possible obs: 93.1 % / Redundancy: 5.2 % / Rsym value: 0.115 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.106 Å / Num. unique obs: 778 / CC1/2: 0.5725

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
AutoProcessdata scaling
AutoProcessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP7

3op7


Resolution: 2.1→73.23 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 3660 4.88 %
Rwork0.22 71388 -
obs0.2211 75048 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.31 Å2 / Biso mean: 32.7388 Å2 / Biso min: 17.03 Å2
Refinement stepCycle: final / Resolution: 2.1→73.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11068 0 5 103 11176
Biso mean--30.4 26.39 -
Num. residues----1395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.31641500.29342801295197
2.13-2.160.30951550.2792884303997
2.16-2.190.31751500.26662817296797
2.19-2.220.34161500.2982895304597
2.22-2.250.2888320.295686789929
2.25-2.290.30881490.26292830297997
2.29-2.330.27681520.24772846299897
2.33-2.370.31091410.23512882302398
2.37-2.420.27451300.24152861299198
2.42-2.470.22571350.24242886302198
2.47-2.520.30111460.25212929307598
2.52-2.580.27391490.25082858300798
2.58-2.640.27441540.25512927308198
2.64-2.720.29281510.25342845299698
2.72-2.80.29481300.24342917304798
2.8-2.890.29811400.24582936307698
2.89-2.990.24031500.24482869301999
2.99-3.110.25381470.22772899304699
3.11-3.250.27531290.23262941307099
3.25-3.370.26981320.22712080221296
3.47-3.640.21291290.21492164229398
3.64-3.920.20441430.20682904304798
3.92-4.310.19191300.17622897302797
4.31-4.930.21241720.17052853302597
4.93-6.210.18861630.19822879304297
6.22-73.230.18631510.17832921307297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00810.01590.24531.3206-0.0021.1545-0.03130.0501-0.02710.03020.0301-0.0205-0.12020.0811-0.00370.1532-0.01170.01260.18470.0190.1628-26.14030.1942-17.3179
21.05660.31460.39950.82140.09931.4001-0.09530.09670.0542-0.17280.12710.0038-0.34990.1069-0.03880.3089-0.03620.0110.24610.02150.2032-33.3576-0.5131-52.4068
30.81950.2194-0.29271.5229-0.12151.1551-0.09480.0084-0.0318-0.09170.0381-0.14720.1830.0160.04220.1878-0.0030.00510.20350.00170.2146-56.5217-38.5464-49.1395
41.0709-0.1409-0.47050.86670.04461.4014-0.123-0.1746-0.11460.19390.1323-0.02450.3730.088-0.02540.32230.0439-0.02590.27210.02950.2194-63.7171-37.8698-13.9261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A18 - 401
2X-RAY DIFFRACTION2chain 'B'B17 - 401
3X-RAY DIFFRACTION3chain 'C'C19 - 401
4X-RAY DIFFRACTION4chain 'D'D18 - 401

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