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- PDB-7r38: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyr... -

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Basic information

Entry
Database: PDB / ID: 7r38
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with S-inosyl-L-homocysteine
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-SIB / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.3Oct 23, 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)101,3386
Polymers99,2412
Non-polymers2,0984
Water5,621312
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,67612
Polymers198,4814
Non-polymers4,1958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area27040 Å2
ΔGint-131 kcal/mol
Surface area50790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.683, 111.683, 121.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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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-SIB / (2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID


Type: L-peptide linking / Mass: 385.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 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: 2.05→82.254 Å / Num. obs: 48734 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.5
Reflection shellResolution: 2.05→2.085 Å / Num. unique obs: 2405 / CC1/2: 0.86

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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: 2.05→53.4 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 2539 5.22 %
Rwork0.1762 46114 -
obs0.1784 48653 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 140 312 7100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236926
X-RAY DIFFRACTIONf_angle_d0.57149354
X-RAY DIFFRACTIONf_chiral_restr0.04241036
X-RAY DIFFRACTIONf_plane_restr0.00331178
X-RAY DIFFRACTIONf_dihedral_angle_d7.7714936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.24561460.22062532X-RAY DIFFRACTION99.93
2.09-2.130.24851340.20712519X-RAY DIFFRACTION100
2.13-2.180.25451170.20792562X-RAY DIFFRACTION99.93
2.18-2.230.25831380.19212517X-RAY DIFFRACTION99.92
2.23-2.280.26651460.20162531X-RAY DIFFRACTION99.85
2.28-2.350.25931440.19422521X-RAY DIFFRACTION99.93
2.35-2.420.26661220.19372562X-RAY DIFFRACTION99.93
2.42-2.490.25541380.19412549X-RAY DIFFRACTION99.85
2.49-2.580.29361180.19852521X-RAY DIFFRACTION98.4
2.58-2.690.22911510.19612530X-RAY DIFFRACTION99.74
2.69-2.810.24151710.18832528X-RAY DIFFRACTION99.96
2.81-2.960.24111640.19332531X-RAY DIFFRACTION99.89
2.96-3.140.26091260.20392574X-RAY DIFFRACTION99.82
3.14-3.380.2491300.19072609X-RAY DIFFRACTION99.71
3.38-3.720.22341700.1662521X-RAY DIFFRACTION98.86
3.72-4.260.18891300.15442601X-RAY DIFFRACTION98.95
4.26-5.370.1431430.14412644X-RAY DIFFRACTION99.64
5.37-53.40.19161510.15812762X-RAY DIFFRACTION98.75
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)
12.691103239980.215691610640.3661643566022.18887489506-0.2187447601141.60134936285-0.00247911523925-0.1040206792760.0983049544160.1109811549850.006890327852370.2316754995170.086201166578-0.1138015604340.01411584546510.157557776664-0.02123532369840.04565819565380.2535762784470.0266792181370.21150549453321.0094485478-9.1413762200957.1528399109
20.8199484085670.2573043737290.9118479616862.481626210150.4841163525981.61601337290.03737300444730.05825745506180.0656032572422-0.1172444229090.05273745335580.276444362624-0.0399888738844-0.153555397157-0.09048619882550.19332579934-0.02721229720690.01958017107040.3002123422070.04292348661180.31785976313116.3378320661-6.7601559565446.4866100078
31.61654026025-0.977118948639-0.2379974900871.083663776170.06083770539570.5877182812570.0166515402864-0.0571457208304-0.008277225574130.02731185911160.03479988151870.21281631324-0.0993408823243-0.138108157377-0.04837595896160.188188401442-0.0235281519707-0.005188081026110.229718054530.02218513985260.24549813167632.58925297272.4906306761541.2584967504
40.9863454642710.239338455426-0.3052982700962.16499474198-0.4718922478721.24164213189-0.007623656279060.1111844475550.026642754001-0.2003794667760.06056287162190.1123736349670.0900535472493-0.147755524607-0.0570032289110.233102317213-0.0162761945778-0.01960493730630.2667668754510.0100416827820.23365791387938.0858718469-6.6172735453627.7395683799
57.90044972714-5.264105868720.745729774274.92721249153-0.5685206340323.56629135684-0.0706025302245-0.3408219690740.235115005620.3283369556290.1080374568110.278366876669-0.500857859399-0.255452471579-0.08819071044050.330271704025-0.04335724340620.0509970103570.2773795665870.01706309022230.41880458284723.04310236746.4331182638655.6675245548
65.03824630737-5.599597797116.424807034977.68518734008-6.585001132697.93118574759-0.542177011625-0.2114152934860.3931860183240.5583528484710.2780530642630.0611301389763-1.39859571956-0.08506213804520.3646361541860.382630564413-0.04735150460960.0382791847410.354758747052-0.0111217091630.34051736191428.866784319711.809250015256.3370083267
70.8384373106321.32925060227-0.2152027568643.8987286339-1.815965358612.573698427450.0793283900432-0.2075690362890.2543058741470.9988324800130.03182921274140.604596707249-0.584329370683-0.153224689755-0.05199865022270.3991368672420.02728473946710.02165222392760.443767725087-0.05757141229040.39767731152546.144562767724.60394199763.9982796642
83.534176580412.08206505245-1.001673085125.68753525278-4.184667733896.314787712570.127730566124-0.0281554583172-0.12966107001-0.1003810505610.2543507149370.5539308624410.473972279919-0.497165201107-0.3744481746170.288595219952-0.0464119449207-0.04849693437830.304343780358-0.05079478057190.33757557438239.8500941358-35.630178499436.5912385491
92.54872051516-0.895034338791-1.130010424837.200056135571.351289006762.471480536440.002459015280470.26261439407-0.275722536781-0.547844588860.0550324928836-0.161562625558-0.04686067299380.160025716314-0.03395041186050.178874546649-0.0186825238854-0.07368013825850.297065478494-0.04789870133680.28304604065656.3160227607-34.924531887329.7810779018
103.09014767192-0.103610318613-0.2206373478590.767034908153-0.02392746066162.631804010940.0594889032453-0.182596541065-0.2320359556010.07210465487150.0428586607809-0.07765372070070.391313670034-0.0299257663457-0.09294423326110.307580531663-0.0184436963844-0.05312585226960.2054202906350.01314564206660.29960114431450.9799328233-39.957636220743.7289196879
111.23951591395-0.565175706874-0.160464847041.452294568840.1525038527360.8616565792660.00989117197422-0.00433860860015-0.130634594035-0.03235985996510.0226253769279-0.1712137906960.1706337517090.178677591957-0.03176035081510.2315837102790.00597172197863-0.01759051054570.2856365924330.008067944204720.28962581134559.4728538835-23.166997965749.0312575702
123.267276053040.532806432109-0.2157512531140.768768587387-0.04251295334040.9639871744620.0484087205146-0.284893625177-0.1459928003850.0166003886455-0.041775626115-0.07713195117330.06785133606290.0473992186004-0.0004085410236630.227607017798-0.0104212279276-0.01644353774110.2610047071990.03706548324620.19824631576253.8602852309-16.765670843664.1598646749
133.62299539326-0.453078554178-3.559901111242.212222058310.9364355727688.020422801870.128234739624-0.377591706291-0.2426685488140.139428211811-0.0207089492280.1181124235130.0986309652970.200747578556-0.1046953607360.211923512894-0.0429874403404-0.03078750802120.2101251556530.04008112157540.23616877627942.252748516-21.140918971759.5939918124
144.50012943166-2.64052937607-0.7989626988242.422421163191.201412004263.691212851020.03047654814560.3527952570340.0535877430422-0.1695580588240.0376147354409-0.4384214323020.2168901279920.443990633296-0.09484072661560.249411771569-0.01784463640680.003408433897890.305078355493-0.04156128976560.35280369012463.6212504059-32.340557277534.3054866984
156.05889052881-5.530371116995.024329703538.16384646891-6.573773790025.481330159280.1926059270540.2983467580720.324477369436-0.343008842889-0.476315051184-0.7119719767320.4904957621620.9060411963170.2127612353880.3717057151240.02677487386090.05137447762650.435234261751-0.07647093196280.37428269855568.7453160745-26.355795319333.7702464728
166.975333722971.287889602391.828065726730.380564736163-0.2110319764152.541397074140.09691273720220.53813801495-0.534867954031-0.1975993544720.141026463961-0.103392906980.1903249240390.379279646807-0.2331669440870.3456515114340.04724416614260.04428504270720.318793591175-0.06582411656560.30424056626780.5375655147-8.5241024131426.4687244752
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 57 )AA1 - 571 - 57
22chain 'A' and (resid 58 through 139 )AA58 - 13958 - 139
33chain 'A' and (resid 140 through 242 )AA140 - 242140 - 242
44chain 'A' and (resid 243 through 351 )AA243 - 351243 - 351
55chain 'A' and (resid 352 through 375 )AA352 - 375352 - 375
66chain 'A' and (resid 376 through 398 )AA376 - 398376 - 398
77chain 'A' and (resid 399 through 421 )AA399 - 421399 - 421
88chain 'B' and (resid 1 through 28 )BE1 - 281 - 28
99chain 'B' and (resid 29 through 57 )BE29 - 5729 - 57
1010chain 'B' and (resid 58 through 139 )BE58 - 13958 - 139
1111chain 'B' and (resid 140 through 242 )BE140 - 242140 - 242
1212chain 'B' and (resid 243 through 316 )BE243 - 316243 - 316
1313chain 'B' and (resid 317 through 351 )BE317 - 351317 - 351
1414chain 'B' and (resid 352 through 375 )BE352 - 375352 - 375
1515chain 'B' and (resid 376 through 398 )BE376 - 398376 - 398
1616chain 'B' and (resid 399 through 421 )BE399 - 421399 - 421

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