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- PDB-6p3h: Crystal structure of LigU(K66M) bound to substrate -

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Basic information

Entry
Database: PDB / ID: 6p3h
TitleCrystal structure of LigU(K66M) bound to substrate
Components(4E)-oxalomesaconate Delta-isomerase
KeywordsISOMERASE / Lignin degradation / protocatechuate 4 / 5-cleavage pathway / PrpF superfamily / (4E)-oxalomesaconate isomerase mechanism
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / lignin catabolic process / isomerase activity
Similarity search - Function
: / PrpF protein / PrpF protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylic acid / (4E)-oxalomesaconate Delta-isomerase
Similarity search - Component
Biological speciesNovosphingobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsCory, S.A. / Hogancamp, T.N. / Raushel, F.M. / Barondeau, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin.
Authors: Hogancamp, T.N. / Cory, S.A. / Barondeau, D.P. / Raushel, F.M.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (4E)-oxalomesaconate Delta-isomerase
D: (4E)-oxalomesaconate Delta-isomerase
C: (4E)-oxalomesaconate Delta-isomerase
B: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,87114
Polymers151,8494
Non-polymers1,02110
Water27,3111516
1
A: (4E)-oxalomesaconate Delta-isomerase
C: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4357
Polymers75,9252
Non-polymers5115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-40 kcal/mol
Surface area23790 Å2
MethodPISA
2
D: (4E)-oxalomesaconate Delta-isomerase
B: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4357
Polymers75,9252
Non-polymers5115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-41 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.880, 134.000, 168.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

21C-577-

HOH

31C-853-

HOH

41C-913-

HOH

51B-891-

HOH

61B-938-

HOH

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Components

#1: Protein
(4E)-oxalomesaconate Delta-isomerase / OMA isomerase / 1 / 3-allylic isomerase LigU


Mass: 37962.328 Da / Num. of mol.: 4 / Mutation: K66M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. (strain KA1) (bacteria)
Strain: KA1 / Gene: ligU, ORF100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0KJL4, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical
ChemComp-NQM / (1E)-4-oxobut-1-ene-1,2,4-tricarboxylic acid


Mass: 202.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1516 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Well - 1000 mM Sodium citrate tribasic, 100 mM Sodium cacodylate/HCl, pH 6.5 Drop - 100 nL enzyme, 100 nL OMA (5 mM), 500 nL well where the enzyme concentration was 20 mg/mL in 20 mM HEPES/KOH pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.62→39.53 Å / Num. obs: 236378 / % possible obs: 97.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.044 / Rrim(I) all: 0.101 / Net I/σ(I): 8.8 / Num. measured all: 1205841 / Scaling rejects: 251
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.597 / Num. measured all: 57956 / Num. unique obs: 11189 / CC1/2: 0.446 / Rpim(I) all: 0.276 / Rrim(I) all: 0.659 / Net I/σ(I) obs: 2.6 / % possible all: 94.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.33 Å39.46 Å
Translation4.33 Å39.46 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P3K

6p3k


Resolution: 1.62→39.46 Å / SU ML: 0.1694 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.5676
RfactorNum. reflection% reflection
Rfree0.1869 2000 0.85 %
Rwork0.1566 --
obs0.1568 236265 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.43 Å2
Refinement stepCycle: LAST / Resolution: 1.62→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10072 0 62 1516 11650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016610765
X-RAY DIFFRACTIONf_angle_d1.394114723
X-RAY DIFFRACTIONf_chiral_restr0.10181727
X-RAY DIFFRACTIONf_plane_restr0.00882003
X-RAY DIFFRACTIONf_dihedral_angle_d8.96888648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.28341360.287216006X-RAY DIFFRACTION93.7
1.66-1.710.26551390.261416218X-RAY DIFFRACTION95.13
1.71-1.760.25981410.234716432X-RAY DIFFRACTION96.38
1.76-1.810.26351410.219416611X-RAY DIFFRACTION97.07
1.81-1.880.27921410.203316464X-RAY DIFFRACTION96.64
1.88-1.950.23511390.181916334X-RAY DIFFRACTION95.53
1.95-2.040.19721440.162216823X-RAY DIFFRACTION98.06
2.04-2.150.18181440.14816868X-RAY DIFFRACTION98.47
2.15-2.280.16931450.14516953X-RAY DIFFRACTION98.66
2.28-2.460.17461450.144617003X-RAY DIFFRACTION99.02
2.46-2.710.18181410.149116513X-RAY DIFFRACTION95.73
2.71-3.10.18471470.156717187X-RAY DIFFRACTION99.28
3.1-3.90.17141480.135517397X-RAY DIFFRACTION99.74
3.9-39.470.15241490.131117456X-RAY DIFFRACTION97.43
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)
10.6136934223530.3630718273440.03854511590381.325207104020.4165463016290.7675354569020.0340720495634-0.07962077354350.1250932015860.0997365251252-0.07468494096290.0663682046014-0.0858646664281-0.003740622331330.03923928317730.219891108177-0.00890068065341-0.01201077876690.211405031823-0.04110633311750.212333462058-29.130516341323.456084341-89.2290725619
20.9653907563370.1545963328680.1776228979411.2632087832-0.2017592768411.667654926160.165197636713-0.295780389071-0.1414864525340.399008685324-0.07776836392530.1928067865260.0934918856856-0.0551184197769-0.08075688394840.337924784917-0.0645000831971-0.01000449511670.247323210583-0.008626923832240.279095965164-27.772351788314.9072574661-71.1404777693
30.6075533978750.179008741585-0.05520363553210.568585810202-0.1853569798460.609025699817-0.01453362313260.02218224836210.0178875239610.02081193706260.01794995503640.0259275258678-0.0060091150523-0.051498946611-0.006284808405350.1650399641450.0046018767675-0.008181007758170.153437019243-0.002208975218220.15300003939-65.39452356646.9827193376624.2703043545
40.6233609280180.211457822587-0.002790399121460.9991410980970.09795727567170.5099196160320.01734817918370.100313455249-0.1244210496970.00901447051882-0.01866142285110.02557722723220.104705695668-0.0468364416756-0.003239893921190.1845224908310.0014637987511-0.001369695323290.192134558707-0.02036953584040.174662263682-63.5646293378-12.587104958518.5056650227
50.452961040113-0.0855122112313-0.08209337135370.7094182141960.1552994482620.784812732948-0.0192890344806-0.02572975757420.01906559188-0.01942345949990.0215175246363-0.1089467963290.005576260435010.112101808504-0.002708644112940.182217234092-0.001679746199230.00244565835660.1952084285030.001656993269720.188521020218-18.90915270675.22014150018-108.947068069
60.73716318820.0787661777646-0.1297781034171.56606603933-0.2269695110270.5484089310960.0103105832457-0.135054489166-0.173782215033-0.0233086257441-0.053302461335-0.1383153356430.101099164670.09108172547470.03873095213350.1674317891780.005330536872340.003875202880090.1995178905710.03598227189110.177565522081-22.5023253653-13.8161491678-102.838691159
70.714744931234-0.1284727929730.1196033016641.3484040181-0.4467835300320.7732698115180.01714669199980.1209807710220.147443604153-0.0884714663577-0.0166210006763-0.0554730664545-0.0309737037332-0.01158733288840.002538121587110.1683022421130.01049399056210.005524007194540.1827470252410.05153976249150.189285832207-55.554197839624.94742896182.94052046869
81.000548797290.1415748186130.5394024229071.335496151260.2910982839871.410313694190.2350114864220.372322993326-0.253875550366-0.3981483032940.108997740114-0.3695480075980.2065688264450.103160611763-0.1448082641430.3407281293320.06951429531320.005842536437190.280390006495-0.04270068581340.362567652554-54.385981169114.6933165289-14.7314390861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:148)
2X-RAY DIFFRACTION2(chain A and resid 149:358)
3X-RAY DIFFRACTION3(chain B and resid 8:177)
4X-RAY DIFFRACTION4(chain B and resid 178:358)
5X-RAY DIFFRACTION5(chain C and resid 7:177)
6X-RAY DIFFRACTION6(chain C and resid 178:358)
7X-RAY DIFFRACTION7(chain D and resid 8:178)
8X-RAY DIFFRACTION8(chain D and resid 179:358)

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