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- PDB-9da1: Crystal structure of human DNPH1 bound to inhibitor 1a -

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Basic information

Entry
Database: PDB / ID: 9da1
TitleCrystal structure of human DNPH1 bound to inhibitor 1a
Components5-hydroxymethyl-dUMP N-hydrolase
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth ...purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
: / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWagner, A.G. / Schramm, V.L. / Almo, S.C. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041916 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD020068 United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Transition State Analogs of Human DNPH1 Reveal Two Electrophile Migration Mechanisms.
Authors: Wagner, A.G. / Lang, T.B.D. / Ledingham, E.T. / Ghosh, A. / Brooks, D. / Eskandari, R. / Suthagar, K. / Almo, S.C. / Lamiable-Oulaidi, F. / Tyler, P.C. / Schramm, V.L.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-hydroxymethyl-dUMP N-hydrolase
B: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1574
Polymers32,4482
Non-polymers7082
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-33 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.761, 64.833, 128.480
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-370-

HOH

21B-328-

HOH

31B-384-

HOH

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Components

#1: Protein 5-hydroxymethyl-dUMP N-hydrolase / 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / c-Myc-responsive protein RCL


Mass: 16224.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Plasmid: pET-28a(+) / Details (production host): LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-A1BBB / 5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate) / 5-(hydroxymethyl)uridine 5'-monophosphate


Mass: 354.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25.1% (w/v) PEG 3350, 2.73% (v/v) Methanol and Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.47→22.82 Å / Num. obs: 43023 / % possible obs: 99.7 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 0.99 / Net I/σ(I): 14.8 / Num. measured all: 404482
Reflection shellResolution: 1.47→1.5 Å / % possible obs: 94.4 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.776 / Num. measured all: 18516 / Num. unique obs: 1960 / CC1/2: 0.846 / Rpim(I) all: 0.261 / Rrim(I) all: 0.82 / Χ2: 1.11 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→22.82 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1786 2192 5.1 %
Rwork0.1532 --
obs0.1545 42971 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→22.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 46 217 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.182
X-RAY DIFFRACTIONf_dihedral_angle_d10.92304
X-RAY DIFFRACTIONf_chiral_restr0.081308
X-RAY DIFFRACTIONf_plane_restr0.016374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.18321260.19212374X-RAY DIFFRACTION95
1.51-1.540.18961290.16812542X-RAY DIFFRACTION100
1.54-1.580.1841400.16282530X-RAY DIFFRACTION100
1.58-1.620.18421770.15442465X-RAY DIFFRACTION100
1.62-1.670.19971350.15732523X-RAY DIFFRACTION100
1.67-1.720.1951280.15832553X-RAY DIFFRACTION100
1.72-1.790.21381450.15292556X-RAY DIFFRACTION100
1.79-1.860.16031460.1492515X-RAY DIFFRACTION100
1.86-1.940.17241230.15542564X-RAY DIFFRACTION100
1.94-2.040.15891240.14622533X-RAY DIFFRACTION100
2.04-2.170.16841240.14972589X-RAY DIFFRACTION100
2.17-2.340.16491250.14822582X-RAY DIFFRACTION100
2.34-2.570.1641350.14572550X-RAY DIFFRACTION100
2.57-2.950.18891480.15472600X-RAY DIFFRACTION100
2.95-3.710.17621270.15072617X-RAY DIFFRACTION100
3.71-22.820.18471600.15552686X-RAY DIFFRACTION100
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)
11.02610.34210.58722.1262-0.43321.8841-0.06060.03140.11270.05620.04180.1107-0.2313-0.03740.02160.14350.00730.0080.115-0.00950.1092-21.2455-4.7829-6.8616
25.22396.03433.73268.42134.48842.69230.156-0.5955-0.18290.6186-0.6860.5783-0.0257-0.56570.24370.2691-0.00430.04350.2730.00620.2515-28.844-1.858-9.5004
32.9163-0.0813-0.46253.2958-4.26815.786-0.08650.0245-0.12030.09550.21310.5786-0.069-0.4509-0.2410.14810.02110.00590.2077-0.00430.2576-34.2903-13.0861-12.9587
41.13020.4439-0.29272.96160.18070.852-0.02230.10080.046-0.19680.06060.0567-0.0815-0.0951-0.03780.107-0.0030.00680.13780.00250.0745-21.659-12.1059-16.0607
52.96170.39064.25324.08250.45576.3178-0.08750.08940.0226-0.44680.1750.1222-0.458-0.1336-0.05650.1755-0.01160.02740.16010.02210.1093-20.2627-6.4602-20.2482
62.45630.6902-0.25794.91831.14753.0303-0.03330.07040.1052-0.36220.0243-0.3353-0.23360.06780.00140.119-0.02780.04870.1559-0.00280.1482-10.7676-8.9907-18.2338
76.5214-0.43142.14993.444-1.2147.5907-0.13340.15840.4511-0.22260.1793-0.2031-0.53210.40920.10190.3041-0.06260.04320.1365-0.00330.1717-13.19443.47-12.072
81.95150.25731.02143.5170.22922.1981-0.02120.3053-0.5717-0.30060.0329-0.18680.32840.0445-0.0510.17330.00040.07010.1917-0.07670.2402-15.5626-34.4308-20.8955
92.41964.19542.16858.94053.48842.1023-0.0160.4515-0.3142-0.42030.277-0.8259-0.01090.4306-0.23780.35330.03910.07020.4155-0.11470.4558-17.4069-33.9045-29.6743
108.15923.76471.34393.55360.42752.13890.11151.0586-0.0164-0.48390.185-0.1256-0.20240.3875-0.29190.31680.00030.06640.3533-0.03340.1364-15.6539-20.8036-30.9554
111.7435-0.00940.01662.3122-0.38781.82630.0030.1491-0.1144-0.1775-0.00530.13780.0755-0.0357-0.01180.0878-0.0086-0.00490.1174-0.0180.0972-24.1491-26.2254-16.9578
122.55730.32910.00213.04350.51183.29080.00850.3024-0.3765-0.12840.01210.03790.4007-0.1382-0.02430.1825-0.0562-0.00280.1783-0.03880.235-28.5217-37.2048-16.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 159 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 48 )
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 72 )
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 134 )
12X-RAY DIFFRACTION12chain 'B' and (resid 135 through 159 )

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