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- PDB-7r37: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyr... -

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Basic information

Entry
Database: PDB / ID: 7r37
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with inosine
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 ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / INOSINE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsSaleem-Batcha, R. / Popadic, D. / Andexer, J.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966 Germany
CitationJournal: Commun Biol / Year: 2024
Title: Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases.
Authors: Koeppl, L.H. / Popadic, D. / Saleem-Batcha, R. / Germer, P. / Andexer, J.N.
History
DepositionFeb 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 18, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)101,1046
Polymers99,2412
Non-polymers1,8634
Water2,036113
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,20812
Polymers198,4814
Non-polymers3,7278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area29080 Å2
ΔGint-127 kcal/mol
Surface area51490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.531, 112.531, 122.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n

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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-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
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: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→48.62 Å / Num. obs: 36380 / % possible obs: 99.82 % / Redundancy: 12.7 % / Biso Wilson estimate: 40.35 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.8
Reflection shellResolution: 2.28→2.41 Å / Num. unique obs: 5179 / CC1/2: 0.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5axa

5axa


Resolution: 2.28→48.62 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1826 5.03 %RANDOM
Rwork0.1613 34493 --
obs0.164 36319 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.14 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 126 113 6887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696918
X-RAY DIFFRACTIONf_angle_d0.85019344
X-RAY DIFFRACTIONf_chiral_restr0.05141034
X-RAY DIFFRACTIONf_plane_restr0.00661178
X-RAY DIFFRACTIONf_dihedral_angle_d7.2497932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.32041410.25292568X-RAY DIFFRACTION98.54
2.35-2.420.30941540.22852593X-RAY DIFFRACTION99.96
2.42-2.490.23961420.20172604X-RAY DIFFRACTION99.96
2.49-2.580.23911140.18722621X-RAY DIFFRACTION100
2.58-2.690.27421530.18762619X-RAY DIFFRACTION100
2.69-2.810.25351330.18482633X-RAY DIFFRACTION99.96
2.81-2.960.23991500.1822615X-RAY DIFFRACTION100
2.96-3.140.25451400.18552658X-RAY DIFFRACTION100
3.14-3.380.22341410.17292631X-RAY DIFFRACTION100
3.38-3.720.21021450.1522664X-RAY DIFFRACTION100
3.72-4.260.19421440.13612679X-RAY DIFFRACTION100
4.26-5.370.18721250.13032743X-RAY DIFFRACTION99.97
5.37-48.620.16551440.14392865X-RAY DIFFRACTION99.7
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)
16.261287340970.02858084974740.7114668138673.11364496724-0.2872369052593.24376338604-0.03669989663090.0329776780098-0.642225911295-0.1457519546270.07811018016180.402411504340.458707563621-0.185017139342-0.006003825673270.315280609648-0.02315066598340.05509731246780.3016803421170.01347411204510.39761281688921.4537613195-17.736520927654.2304781901
24.95577321436-0.4655512072520.02036584556662.4223573756-0.2743236258451.739317200980.0101904848859-0.57690545632-0.1216343339230.340274056831-0.01909633035020.285314245519-0.108130984522-0.1950250337010.02981519715130.297605033835-0.02267958600920.04330261678090.3832320517920.01355651702310.3903513938521.1133187166-1.0387636529260.9191609119
31.08986522801-0.1618370032710.5497103981152.864369982410.2872838534121.653115341240.06661662117480.0560040756858-0.142468681517-0.124284094967-0.03223986350230.6028858089410.0482611186765-0.338102462037-0.03199150741180.275658916567-0.022521357904-0.02081999324760.4144875175480.02167799790210.51619656403816.5206019736-6.8150301067746.9183678668
40.328211274195-0.2746046356890.2724892134532.6773779549-0.6438917787874.208179546220.2217758519380.102441873856-0.1090150242550.00670913494092-0.05746851624670.836071428654-0.264428637855-0.480043166513-0.1136873389840.3385792987680.02942692600910.002209487006340.484707709738-0.03746512588830.59358454259116.09766547557.7074924421442.7155292188
51.32909916474-0.746296783608-0.14690825181.38679206254-0.1204349200710.7160396114340.0890330681649-0.152063098850.0825264813779-0.101671198529-0.008499270317920.177327115779-0.0641352148725-0.0948072766272-0.06701189730140.274499933376-0.0263568957442-0.04050422002320.315167988940.02082170550330.29993610546840.29217945381.7103179882240.461625445
62.37554480197-0.267143867220.5001743524393.0828480596-0.04537038998022.789784376940.03806755478450.2605658200540.0472567698186-0.4696875518040.0592325592830.177332138504-0.110770723345-0.301077009825-0.1051257483270.34476467980.00308868099553-0.06521029693660.317381364160.02652914038130.2366374492738.4589138053-4.7834415317325.4418995836
72.02185675117-0.179315977444-0.4294215405963.039713839542.384883995264.99099295536-0.131550592110.175367651252-0.213477109848-0.399275990351-0.0285446420010.3505073768310.0812284404249-0.2373751111030.1430385871610.353617574499-0.0373816673307-0.06651154283230.3147629991190.02722464291680.24657802446335.8207236734-14.636022339931.1680662663
86.53655711007-3.00256030864-0.3261411508787.36234506019-0.1439334739054.10154854405-0.0605516847155-0.1391987237390.06890805861760.191392644846-0.06862295099910.702383993196-0.466286826225-0.3723373612020.1055044959860.377102274978-0.02577644130830.05071986484560.358309275084-0.01689734416820.42518772063223.37194900266.4308065530456.0510460419
99.07647647413-4.673244091097.670447560014.79236904618-4.040058622319.49941654321-0.514666441673-0.4516923258650.5558368864790.5961821435860.3014453092280.0910124672227-1.17485845511-0.369870929210.3225500711920.430889709396-0.06711828945530.08176896836710.466611792375-0.02438706444920.40957234393929.033911979811.717206456756.7588613685
101.358259097920.939770990561-0.1364788313172.06620223334-0.6831379740862.255566812460.0935974466871-0.432871083370.4781565205121.225082470730.2113664714820.533344812533-0.610496476462-0.210310029527-0.3223617696080.5008110651150.07709731854510.07827228831010.570095813192-0.1000553188210.54401978375846.565293373624.484524593264.383681849
112.175127905091.61449937147-0.2930620102755.51574361618-1.415814564932.13385196080.0965479566823-0.233352070192-0.167198554186-0.203808942726-0.05774819946260.3077242457730.154031144724-0.216939251153-0.07278658313670.359979020383-0.0605518009158-0.1039428965870.393109279073-0.02656230465470.38986233450240.338212308-35.747276024436.7881242744
122.35858172735-0.984115167201-0.2652270370174.779470174810.1377221520691.674831305620.0821514001880.326704653188-0.404024938412-0.512732199628-0.0217298118617-0.2140155465460.2952285920020.186439270235-0.02729532659780.399324768660.0234880618943-0.07141324125520.370798010931-0.06835810027190.41830414645456.8247409144-34.911117054330.0367787553
132.309369165470.9201306847320.6970931291460.8250261152680.310931996882.738747374910.0265202986904-0.143318185102-0.4756935466360.08161516070130.13088794399-0.1755987119650.4704296016230.0316031647115-0.1728563112330.4297367322270.0512518131405-0.05945691715890.3085098658430.01671926358470.48527124698355.3230213363-39.967883010944.9735836374
142.64689126554-1.618169850740.4421866187424.65576650991-0.721482772041.514023734520.0685178060001-0.0224183544312-0.2481031609520.139281669883-0.0563036307185-0.04880944923140.1130977793140.314919395763-0.00347312074690.367294277672-0.0193737298086-0.01420207535160.3315736111270.01090230393510.4214114447166.7534407867-28.179744580744.1896328033
152.153407379450.275105998157-0.01255191865131.56096517948-0.3883577374041.33669449440.0542277804385-0.362612427459-0.1035825807490.173768326774-0.024338295348-0.1075276332520.1108612981450.0678709357353-0.02891872756250.258344674981-0.00317305159537-0.02579810709810.3283923744270.0294261251110.24083043266853.8117325588-14.701731861959.7593671197
163.515591089620.227424299926-2.198902180261.82477984021-0.06501535603894.67860662410.118310721004-0.579498944719-0.1490058298730.0889307397051-0.01523535538740.0700187899527-0.1161524335080.0917385217119-0.03082023369970.303009133804-0.0308068939667-0.03307706863830.3817055880310.06361748196150.29980967977242.6196658123-21.127002928959.9125490201
173.99743555117-2.62807763167-0.7815311182837.986075463660.1016075253453.814283055980.02429869487190.533147559082-0.485372396889-0.344868207722-0.222423811198-0.3787820695410.3955957217160.38792351680.1682953629790.3949471015240.02148372327710.01521774020280.384597105006-0.05597788398270.38845590374864.1468393075-32.233539547634.6033792893
184.62325070877-4.017731153314.071223380428.39947531919-7.038716585418.059621926250.1546019428120.6341831427410.103695058701-0.199024215952-0.744064129774-0.7449982381150.3614935537561.213216234520.5363338080170.4003888696950.01894883809640.06028940386170.484940092048-0.04124328556620.42778189057969.2793234734-26.346633249934.0948013656
192.51559183240.8216070054181.14400089950.756200350962-0.4834971104252.187908769910.2634782404151.0146263059-0.389989423676-0.164655617785-0.00744000771949-0.2769119499760.205291718610.614463221729-0.2533240900880.4247015247430.07193883741650.07750687802350.462236891459-0.03067279088920.43227120820381.1041893024-8.5809934408726.6863229243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 28 )AA1 - 281 - 28
22chain 'A' and (resid 29 through 57 )AA29 - 5729 - 57
33chain 'A' and (resid 58 through 139 )AA58 - 13958 - 139
44chain 'A' and (resid 140 through 166 )AA140 - 166140 - 166
55chain 'A' and (resid 167 through 251 )AA167 - 251167 - 251
66chain 'A' and (resid 252 through 316 )AA252 - 316252 - 316
77chain 'A' and (resid 317 through 351 )AA317 - 351317 - 351
88chain 'A' and (resid 352 through 375 )AA352 - 375352 - 375
99chain 'A' and (resid 376 through 398 )AA376 - 398376 - 398
1010chain 'A' and (resid 399 through 421 )AA399 - 421399 - 421
1111chain 'B' and (resid 1 through 28 )BE1 - 281 - 28
1212chain 'B' and (resid 29 through 57 )BE29 - 5729 - 57
1313chain 'B' and (resid 58 through 166 )BE58 - 16658 - 166
1414chain 'B' and (resid 167 through 189 )BE167 - 189167 - 189
1515chain 'B' and (resid 190 through 316 )BE190 - 316190 - 316
1616chain 'B' and (resid 317 through 351 )BE317 - 351317 - 351
1717chain 'B' and (resid 352 through 375 )BE352 - 375352 - 375
1818chain 'B' and (resid 376 through 398 )BE376 - 398376 - 398
1919chain 'B' and (resid 399 through 421 )BE399 - 421399 - 421

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