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- PDB-9ifa: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyr... -

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Basic information

Entry
Database: PDB / ID: 9ifa
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with hypoxanthine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Complex / S-adenosyl-L-homocysteine (SAH) / S-adenosyl-L-methionine (SAM)
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
HYPOXANTHINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.064 Å
AuthorsSaleem-Batcha, R. / Koeppl, L.H. / Andexer, J.N.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966European Union
CitationJournal: To Be Published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with hypoxanthine
Authors: Saleem-Batcha, R. / Koeppl, L.H. / Andexer, J.N.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8406
Polymers99,2412
Non-polymers1,5994
Water2,540141
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,67912
Polymers198,4814
Non-polymers3,1988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area28310 Å2
ΔGint-118 kcal/mol
Surface area50780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.929, 111.929, 121.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 421 / Label seq-ID: 21 - 441

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 49620.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: ahcY, PF0343 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50251, adenosylhomocysteinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: comprising 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→48.31 Å / Num. obs: 45682 / % possible obs: 94.8 % / Redundancy: 22.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.7
Reflection shellResolution: 2.06→2.12 Å / Num. unique obs: 2369 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.064→48.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.532 / SU ML: 0.118 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.206 2151 4.714 %
Rwork0.165 43482 -
all0.167 --
obs-45633 94.594 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.064→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 108 141 6895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166696
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.8429303
X-RAY DIFFRACTIONr_angle_other_deg0.5461.77915427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.465551
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.481101277
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.37410301
X-RAY DIFFRACTIONr_chiral_restr0.0750.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
X-RAY DIFFRACTIONr_nbd_refined0.2110.21400
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.26238
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23413
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.258
X-RAY DIFFRACTIONr_nbd_other0.1610.2259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.229
X-RAY DIFFRACTIONr_mcbond_it2.6993.5113368
X-RAY DIFFRACTIONr_mcbond_other2.6993.5113368
X-RAY DIFFRACTIONr_mcangle_it3.6326.2984207
X-RAY DIFFRACTIONr_mcangle_other3.6326.2994208
X-RAY DIFFRACTIONr_scbond_it4.6884.1793525
X-RAY DIFFRACTIONr_scbond_other4.6884.1793526
X-RAY DIFFRACTIONr_scangle_it7.0047.3865095
X-RAY DIFFRACTIONr_scangle_other7.0037.3865096
X-RAY DIFFRACTIONr_lrange_it8.10138.1287782
X-RAY DIFFRACTIONr_lrange_other8.137.827771
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.0513930
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.065930.05009
12AX-RAY DIFFRACTIONLocal ncs0.065930.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.064-2.1170.3161200.292096X-RAY DIFFRACTION63.4049
2.117-2.1750.3231080.2272624X-RAY DIFFRACTION79.5574
2.175-2.2380.2191190.2112766X-RAY DIFFRACTION86.5327
2.238-2.3070.2561290.1972917X-RAY DIFFRACTION95.128
2.307-2.3820.2221580.1862990X-RAY DIFFRACTION99.7465
2.382-2.4660.2231560.1642884X-RAY DIFFRACTION100
2.466-2.5580.2251340.1532790X-RAY DIFFRACTION100
2.558-2.6620.2241270.1722718X-RAY DIFFRACTION100
2.662-2.7810.2371360.1652581X-RAY DIFFRACTION99.9264
2.781-2.9160.2331350.1832455X-RAY DIFFRACTION99.9614
2.916-3.0730.2291300.1792351X-RAY DIFFRACTION100
3.073-3.2580.2481110.1792249X-RAY DIFFRACTION100
3.258-3.4820.2271050.1662133X-RAY DIFFRACTION100
3.482-3.760.162680.1472016X-RAY DIFFRACTION100
3.76-4.1160.196960.1371821X-RAY DIFFRACTION100
4.116-4.5980.1451040.1271648X-RAY DIFFRACTION100
4.598-5.3010.149870.1361494X-RAY DIFFRACTION99.9368
5.301-6.4730.227660.1561269X-RAY DIFFRACTION100
6.473-9.0730.196370.151038X-RAY DIFFRACTION99.8143
9.073-48.310.181250.206642X-RAY DIFFRACTION100

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