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- PDB-7uut: Ternary complex crystal structure of secondary alcohol dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 7uut
TitleTernary complex crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus mutants C295A and I86A provides better understanding of catalytic mechanism
Components(Secondary-alcohol ...) x 2
KeywordsOXIDOREDUCTASE / secondary alcohol dehydrogenases / NADP / 2-pentanol
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2R)-pentan-2-ol / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDinh, T. / Phillips, R. / Rahn, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2022
Title: Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network.
Authors: Dinh, T. / Rahn, K.T. / Phillips, R.S.
History
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionMay 11, 2022ID: 7JNU
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity_src_gen.gene_src_common_name ..._entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jul 20, 2022Group: 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secondary-alcohol dehydrogenase
B: Secondary-alcohol dehydrogenase
C: Secondary-alcohol dehydrogenase
D: Secondary-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,43920
Polymers150,6954
Non-polymers3,74416
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.870, 124.560, 166.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 55 or resid 57...
d_2ens_1(chain "B" and (resid 2 through 55 or resid 57...
d_3ens_1(chain "C" and (resid 2 through 55 or resid 57...
d_4ens_1(chain "D" and (resid 2 through 55 or resid 57...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSMETA2 - 55
d_12ens_1LEUALAA57 - 61
d_13ens_1GLYASPA63 - 79
d_14ens_1VALPROA81 - 88
d_15ens_1TRPTRPA90
d_16ens_1THRSERA92 - 93
d_17ens_1VALILEA95 - 164
d_18ens_1LEULEUA166 - 188
d_19ens_1GLYILEA190 - 223
d_110ens_1SERARGA225 - 313
d_111ens_1ASPSERA315 - 317
d_112ens_1LEUARGA319 - 325
d_113ens_1ASPGLUA328 - 331
d_114ens_1ALALYSA333 - 338
d_115ens_1LYSILEA340 - 350
d_116ens_1ALAALAA352
d_117ens_1ZNZNB
d_118ens_1NAPNAPC
d_119ens_1R2PR2PD
d_21ens_1LYSMETE2 - 55
d_22ens_1LEUALAE57 - 61
d_23ens_1GLYASPE63 - 79
d_24ens_1VALPROE81 - 88
d_25ens_1TRPTRPE90
d_26ens_1THRSERE92 - 93
d_27ens_1VALILEE95 - 164
d_28ens_1LEULEUE166 - 188
d_29ens_1GLYILEE190 - 223
d_210ens_1SERARGE225 - 313
d_211ens_1ASPSERE315 - 317
d_212ens_1LEUARGE319 - 325
d_213ens_1ASPGLUE328 - 331
d_214ens_1ALALYSE333 - 338
d_215ens_1LYSILEE340 - 350
d_216ens_1ALAALAE352
d_217ens_1ZNZNF
d_218ens_1NAPNAPG
d_219ens_1R2PR2PH
d_31ens_1LYSMETI2 - 55
d_32ens_1LEUALAI57 - 61
d_33ens_1GLYASPI63 - 79
d_34ens_1VALPROI81 - 88
d_35ens_1TRPTRPI90
d_36ens_1THRSERI92 - 93
d_37ens_1VALILEI95 - 164
d_38ens_1LEULEUI166 - 188
d_39ens_1GLYILEI190 - 223
d_310ens_1SERARGI225 - 313
d_311ens_1ASPSERI315 - 317
d_312ens_1LEUARGI319 - 325
d_313ens_1ASPGLUI328 - 331
d_314ens_1ALALYSI333 - 338
d_315ens_1LYSILEI340 - 350
d_316ens_1ALAALAI352
d_317ens_1ZNZNJ
d_318ens_1NAPNAPK
d_319ens_1R2PR2PL
d_41ens_1LYSMETM2 - 55
d_42ens_1LEUALAM57 - 61
d_43ens_1GLYASPM63 - 79
d_44ens_1VALPROM81 - 88
d_45ens_1TRPTRPM90
d_46ens_1THRSERM92 - 93
d_47ens_1VALILEM95 - 164
d_48ens_1LEULEUM166 - 188
d_49ens_1GLYILEM190 - 223
d_410ens_1SERARGM225 - 313
d_411ens_1ASPSERM315 - 317
d_412ens_1LEUARGM319 - 325
d_413ens_1ASPGLUM328 - 331
d_414ens_1ALALYSM333 - 338
d_415ens_1LYSILEM340 - 350
d_416ens_1ALAALAM352
d_417ens_1ZNZNN
d_418ens_1NAPNAPO
d_419ens_1R2PR2PP

NCS oper:
IDCodeMatrixVector
1given(-0.999986107419, 0.00526897464284, -0.000151246680783), (0.00411500157507, 0.762401468556, -0.647091235844), (-0.00329419662173, -0.647082868457, -0.76241255867)37.1152935417, -9.21878621551, -24.3100317512
2given(-0.526545052152, 0.312872507371, 0.790481563469), (0.293635205141, -0.805664148533, 0.514474145192), (0.797827471547, 0.503007031661, 0.332348088221)39.4741689807, -3.70874249878, -22.0589721664
3given(0.515426938075, -0.302880510701, -0.801622397232), (-0.305277033728, -0.938981391043, 0.158492523335), (-0.800712810054, 0.163025591586, -0.576438767176)-2.21158929118, 2.70307135082, -5.21690695735

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Components

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Secondary-alcohol ... , 2 types, 4 molecules ABCD

#1: Protein Secondary-alcohol dehydrogenase


Mass: 37652.793 Da / Num. of mol.: 1 / Mutation: I86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)
#2: Protein Secondary-alcohol dehydrogenase


Mass: 37680.801 Da / Num. of mol.: 3 / Mutation: I86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)

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Non-polymers , 5 types, 374 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-2RP / (2R)-pentan-2-ol


Mass: 88.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.6 M KCl, 12% PEG 3350, 50 mM HEPES buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→83.24 Å / Num. obs: 89509 / % possible obs: 94 % / Redundancy: 21.3 % / Biso Wilson estimate: 36.41 Å2 / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 4475 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YKF

1ykf


Resolution: 1.89→39.47 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 1995 2.24 %
Rwork0.1997 87184 -
obs0.2005 89179 67.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.97 Å2
Refinement stepCycle: LAST / Resolution: 1.89→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10566 0 224 358 11148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002911171
X-RAY DIFFRACTIONf_angle_d0.599915177
X-RAY DIFFRACTIONf_chiral_restr0.04721688
X-RAY DIFFRACTIONf_plane_restr0.00431949
X-RAY DIFFRACTIONf_dihedral_angle_d11.22934082
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.542424315594
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.730135329445
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.622971572143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.7232150.5748577X-RAY DIFFRACTION6.34
1.94-1.990.3413240.41741083X-RAY DIFFRACTION11.81
1.99-2.050.3945410.36121762X-RAY DIFFRACTION19.15
2.05-2.120.4599680.35362972X-RAY DIFFRACTION32.28
2.12-2.190.33771000.32144405X-RAY DIFFRACTION48
2.19-2.280.38631290.37935651X-RAY DIFFRACTION61.05
2.28-2.380.32251520.296622X-RAY DIFFRACTION72.03
2.38-2.510.30841810.28147871X-RAY DIFFRACTION85.04
2.51-2.660.34072080.26639141X-RAY DIFFRACTION98.77
2.66-2.870.26122120.24239270X-RAY DIFFRACTION99.92
2.87-3.160.27482130.22459313X-RAY DIFFRACTION100
3.16-3.620.22922130.18989357X-RAY DIFFRACTION100
3.62-4.550.17662160.15179413X-RAY DIFFRACTION100
4.56-39.470.17182230.1479747X-RAY DIFFRACTION99.96
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)
14.003893206110.6486036927750.9023982984160.1059906893060.1834977889130.5800569534650.556473216142-1.50298242265-1.035969924580.42160043654-0.0737501037533-0.2034839569910.8240962920140.0829127490389-0.3876429389531.72507728768-0.677232147124-0.2003227307341.671246969860.2474855896310.52695936464919.8706610122-10.859736109724.6720126325
21.854215972130.4649911177880.3889373263250.6340906473310.3732741030860.9664694504490.676356498277-1.31638967094-0.02441431732961.01238790528-0.3547568227390.09106538426610.06856623558110.132905965966-0.1191425586690.937688660077-0.4043973808940.05907727498390.918794603373-0.06360481104680.20332963269213.4058918808-2.850138378849.96770192412
31.825251289440.0045776346687-0.03339816469450.820380522072-0.03280666913491.805160771730.497757144876-1.00831029011-0.5828279634670.830849758507-0.2805440741310.191773069910.561239625723-0.04656460762150.01966652058750.848687457079-0.3348829877360.07199173035410.755403769490.12658169490.2948816100446.68906485736-14.09950437934.61651407945
43.00182803477-0.4163247331230.514300597634.745695927920.9782416872821.62500187639-0.102430078820.474550568084-0.8713897521970.2083019804580.250574157884-0.06853022553210.217118664871-0.16615448454-0.1150089264380.429760600563-0.0336131262038-0.008064072369270.422689227242-0.2207671826270.4359664879917.1711065701-28.8869614647-38.9527446965
52.088320309120.9135423288550.9080461874341.191881403810.8302447389732.544918547050.1192943620720.170154278407-0.4319398778950.05597396507170.0516735136309-0.2417688591250.156401434501-0.0423041852987-0.14740596680.3344549942110.0204577905764-0.04783780044090.178356659055-0.07281204430820.31435260576824.6341395549-18.0896657775-27.5302919849
62.59755606983-0.133454006056-0.5155179939511.818685629830.04679269058442.944538468410.114918785274-0.540419815393-0.7806972972310.478495719704-0.0606230505261-0.1865218317570.6651661677290.04008468702720.01901142379740.567781392822-0.0489989308665-0.1572994514650.2670932246880.08398548991130.47283897862528.7056511267-20.0997739152-11.1485662459
71.38996570680.473355883733-0.2890071765084.517462212281.893666943671.36860466578-0.06307170724510.592143504684-1.03215144166-0.002360546185160.292312041756-0.4159061640020.3984139906020.16133092306-0.120000000430.4902299799280.0796599028387-0.05463554040040.451665071682-0.3027262450510.8341249898133.5631991857-28.9164545463-35.0856093908
82.827585868071.06909513192-0.4567081042582.02944301266-0.1339625157964.543331722720.450772649189-0.8313161664970.7100673344030.6581927804630.0024074325991-0.0414195659551-0.63243554747-0.105276645312-0.3688740103640.470215792285-0.117209511144-0.06355336996440.508632814528-0.2045091982680.57020250187945.825266697218.9403815635-1.30846858234
92.452304154720.5335656006890.8276537544261.862114733930.1313553045132.725935095390.171832742556-0.3543902830580.2621401257220.376586194982-0.0740311704311-0.167720385339-0.0829496200743-0.0358781393123-0.06334727970260.181304746928-0.024521250649-0.01424339187990.220026821322-0.07401856091170.26007124408137.75965547497.84078519556-11.6801833927
103.81642058249-0.2602626013980.5387898045412.74923459795-0.1947810850821.844784655710.003529167581020.3974734854560.60055256594-0.142567443111-0.05661206900730.0461527027108-0.273682228012-0.07813153904990.0581939266530.172982733026-0.0394830421980.02974301085020.207073543951-0.0007366755612160.24065916307427.700303813810.9497223845-24.5984062315
113.016052028561.75836441793-0.02490695681223.161106043670.2614187072681.644805094390.2095937590050.06760772560940.3935422426310.224122990901-0.0237648252908-0.419808025565-0.1824620347120.196115951759-0.1456460274140.156381451618-0.0380953495448-0.03048409204780.29273603187-0.08260504380930.48005750042751.404306583414.4602416876-17.1821723663
121.79246758833-1.28738792913-0.4837443952392.934267298570.2396480001172.865254346940.188734872680.6459846260630.500700148705-0.311337127915-0.0938304356726-0.118998198348-0.124610257442-0.0599001359488-0.1112648759590.179325006866-0.0221998380331-0.03446743169010.3717016861020.12247976570.504835848488-9.405738140885.71625727101-35.9285315036
131.995062009710.575355492211.112286477271.279392236280.9351337995672.525851567830.100010900592-0.07699715859750.2781971683780.0177846555175-0.05661303227080.1238266843150.09308294615870.00498891816186-0.04703494594340.164948654255-0.02542739865650.04870657810930.161710619956-0.003460847285860.340320326718-1.061738071454.57461834664-20.6718497219
142.216071691610.03093045717910.1687028103362.018673185070.4927301883041.168610515720.0705735161152-0.1630616274190.7669314455940.0516312524805-0.01256442900960.133219394581-0.2383061623040.0213801934208-0.05766516815320.210195975756-0.007362463704710.05423672282120.202461495406-0.0855727972940.3643092323149.5198241848615.4182551243-12.9901138911
153.56988109942-0.79996324649-0.2888507866981.67834269021-0.307915154222.119079025450.1010912039910.04033826038870.8405845074850.01230023390060.01634527486160.417840945946-0.124083902462-0.392966091612-0.06796390152850.132321465314-0.05036825726990.01426389407480.310891206099-0.003066240370520.654747368135-14.566318527112.9047367057-21.0077990305
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 59 )AA1 - 591 - 59
22chain 'A' and (resid 60 through 210 )AA60 - 21060 - 210
33chain 'A' and (resid 211 through 352 )AA211 - 352211 - 352
44chain 'B' and (resid 1 through 79 )BE1 - 791 - 79
55chain 'B' and (resid 80 through 210 )BE80 - 21080 - 210
66chain 'B' and (resid 211 through 310 )BE211 - 310211 - 310
77chain 'B' and (resid 311 through 352 )BE311 - 352311 - 352
88chain 'C' and (resid 1 through 79 )CI1 - 791 - 79
99chain 'C' and (resid 80 through 210 )CI80 - 21080 - 210
1010chain 'C' and (resid 211 through 310 )CI211 - 310211 - 310
1111chain 'C' and (resid 311 through 352 )CI311 - 352311 - 352
1212chain 'D' and (resid 1 through 79 )DM1 - 791 - 79
1313chain 'D' and (resid 80 through 210 )DM80 - 21080 - 210
1414chain 'D' and (resid 211 through 310 )DM211 - 310211 - 310
1515chain 'D' and (resid 311 through 352 )DM311 - 352311 - 352

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