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- PDB-7tcs: M379A mutant tyrosine phenol-lyase complexed with L-methionine -

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Basic information

Entry
Database: PDB / ID: 7tcs
TitleM379A mutant tyrosine phenol-lyase complexed with L-methionine
ComponentsTyrosine phenol-lyase
KeywordsLYASE / pyridoxal-5'-phosphate / mutation / substrate specificity
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
Similarity search - Function
Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / : / PYRIDOXAL-5'-PHOSPHATE / Chem-PN9 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPhillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM137008 United States
CitationJournal: Chembiochem / Year: 2022
Title: M379A Mutant Tyrosine Phenol-lyase from Citrobacter freundii Has Altered Conformational Dynamics.
Authors: Phillips, R.S. / Jones, B. / Nash, S.
History
DepositionDec 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _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: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
C: Tyrosine phenol-lyase
D: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,27922
Polymers205,7954
Non-polymers2,48418
Water30,2831681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-162 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.550, 82.990, 96.580
Angle α, β, γ (deg.)93.730, 105.710, 114.240
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51448.637 Da / Num. of mol.: 4 / Mutation: M379A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 6 types, 1699 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PN9 / (4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl)propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate / PLP-Met adduct intermediate in zwitterionic form


Mass: 378.338 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H19N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1681 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 mM PLP, 1 mM EDTA, 1 mM DTT, 19% PEG 5000 MME, 0.4 M CsCl

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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: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→53.87 Å / Num. obs: 363833 / % possible obs: 87.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 10.46
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 18122 / CC1/2: 0.274

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
autoPROC1.19.2_4158data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLH

2vlh


Resolution: 1.37→45.27 Å / SU ML: 0.1659 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.1939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1549 2001 0.6 %
Rwork0.1412 333282 -
obs0.1413 335283 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 1.37→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14451 0 107 1682 16240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005916342
X-RAY DIFFRACTIONf_angle_d0.904722090
X-RAY DIFFRACTIONf_chiral_restr0.06992355
X-RAY DIFFRACTIONf_plane_restr0.00862889
X-RAY DIFFRACTIONf_dihedral_angle_d12.84056263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.38021200.305918321X-RAY DIFFRACTION72.3
1.4-1.440.29171160.272422969X-RAY DIFFRACTION90.52
1.44-1.480.24171550.228823605X-RAY DIFFRACTION93.32
1.48-1.530.25611430.192123787X-RAY DIFFRACTION93.86
1.53-1.590.18091380.175323933X-RAY DIFFRACTION94.56
1.59-1.650.19181440.166123991X-RAY DIFFRACTION94.95
1.65-1.730.18361410.161524255X-RAY DIFFRACTION95.36
1.73-1.820.16561500.161224254X-RAY DIFFRACTION95.78
1.82-1.930.16881410.15124412X-RAY DIFFRACTION96.19
1.93-2.080.15381530.143224394X-RAY DIFFRACTION96.63
2.08-2.290.16721440.132824617X-RAY DIFFRACTION97.17
2.29-2.620.15181500.129624776X-RAY DIFFRACTION97.7
2.62-3.30.1481520.132924858X-RAY DIFFRACTION98.3
3.3-45.270.12371540.123725110X-RAY DIFFRACTION99.05
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)
10.9271503632340.0529343124325-0.6702663250170.1863885732630.06356622478921.7793699648-0.0400823288870.04411896409310.002959078251110.0190812428004-0.007344933734370.1136189370510.0875343154152-0.1981854037890.04824746447190.1850453879870.000884556269915-0.007470091339340.175381724528-0.00594502819840.221736178265-24.6069803628-1.43572265606-4.97147961749
20.740591077810.223009628273-0.009964882546731.427711348780.4251620866680.560157024304-0.02749377505690.02009342985040.00188821138457-0.04238940364710.0827057951047-0.26490011453-0.01627990392150.0709078575271-0.03909803089290.1700232615580.000399799181635-0.006528314343790.17706468961-0.002097870953650.2013778805092.46495711878-11.1497385271-14.2098837848
30.7648509468180.1642062831070.2571872186930.9084734100050.2445041922181.11614289663-0.00647039881332-0.1127330566650.04760432633620.2727201370480.0339910366933-0.0480660346090.05998993695590.0126790668855-0.03353005318570.227915446230.00261943356197-0.04586496064270.193872079151-0.01357548388750.214328925729-0.6525708724170.79362630436710.8005284222
40.86058207037-0.2601213319040.08640496673121.00788879689-0.4768071839570.838197948522-0.0113078394682-0.1690482927520.1031818235440.2071608702740.00641461816495-0.151961648756-0.06041312355360.1107522350490.01628923871050.225914349122-0.00768340525815-0.05508771637990.208100296718-0.03552075589640.2516737015744.392674762648.361489466437.95680438494
50.4748139378910.2003185112380.09199278380410.9297119858390.4239731206640.5837755065150.0377088287488-0.0003560678207440.03670730393420.1244939386960.0520534469152-0.2354265226460.04174911494710.16268158145-0.07099009563880.164706370547-0.0013493096733-0.0414948322040.168045961812-0.02046291620220.2232696649495.23226063747-1.41929250782-1.57123888629
60.762011469046-0.949776878736-0.06230498890272.225129454820.3672562570240.3647361839-0.0324684958519-0.02079140710990.06661219090340.04570439411090.0676911857035-0.103864932682-0.0113016043510.0243862813923-0.03237327629230.154112029101-0.0132839170795-0.01465049466850.149066590239-0.002250311365950.171128100399-7.003447870071.28879229176-8.79907418427
70.501056094337-0.0980472477299-0.01586115467261.03842659753-0.07552276237140.930080168112-0.0244020704905-0.1460129411540.026585671650.2655876946770.02617934539420.0922003193668-0.0283729663485-0.06200956825710.002618349470960.2428771453970.009118629682170.008022091689030.20018696533-0.01737842965360.207300408608-22.39618587234.60493593389.41820301357
80.651634024753-0.03427516642330.1314408844260.948937912236-0.6523823046641.42424220464-0.04894717388360.05320531860280.192578247270.0261671011139-0.0781121166497-0.190442875638-0.1438443959420.2155593037140.103503112980.164495722689-0.0263188517087-0.02843395799750.1663983939550.01034456973530.236647179696-14.78327378777.70596644666-30.136180113
90.928228070222-0.2844334580490.229768884870.518872398588-0.1199594132620.546017008558-0.0007089114215060.1152291712520.0355812519829-0.0488774332951-0.02357034474910.093675775657-0.0127072307731-0.04330757304240.02019684595830.14443336656-0.0110333821751-0.007907148786690.195050790823-0.005655404486350.191504181049-37.6301716717-5.74961199713-40.980870498
100.498529795761-0.1319275593650.1428063288680.530247770453-0.1010060147220.457608907762-0.04207161001940.1249786133250.165986616787-0.05530706048130.00182111741588-0.0313094818835-0.1349098187240.01007584429330.0410773739740.196384446966-0.00555398361183-0.01783783404940.2048348852430.03065824083260.233163941492-24.25943637910.5837114472-38.0477290072
111.25784379362-0.421199045410.4185545954730.6007694351640.003003118001370.707967681713-0.02084584682340.0682532947940.196393014961-0.043640689441-0.027219627239-0.228475836274-0.04549530604290.1376333976550.03714303641310.1440089367970.003465544595880.02061595773720.1636385104940.0008338947515470.2159476806299.72730559997-27.8267522007-18.6169088779
120.294361266161-0.0919424430084-0.0367273542971.38068919203-0.4969691951440.590795403395-0.0391999627026-0.0168236565758-0.03295508673660.257741003015-0.0224187361983-0.0604579542872-0.03404550877010.06350050408220.05795500523040.212344762475-0.00176642288276-0.005579306951610.149861188599-0.007038044528750.15259772312-8.83099149721-29.44551653892.53736054646
130.526901813037-0.128240937670.01314899627741.19354209854-0.1883577687740.70018967748-0.0552565062801-0.098131525026-0.09516675624220.2095664277520.02451846852780.1324765949240.0821565903481-0.02734472508020.0233740809850.2416645615730.009214615169790.05310632625150.1608079395930.01150130011990.20344233712-11.6020753782-40.09674278745.1069754986
140.449522318908-0.208576536198-0.02858465710231.01364045720.1887499463830.383770752358-0.0404328036543-0.0446549972881-0.0355796670330.1663971389250.0605829849378-0.2539786996510.0923303285910.133578783148-0.01745129150450.169508472780.0279898994427-0.04122974685120.1598817788870.008533299172030.2146757020848.64851109462-34.382472099-4.94801334454
150.8492527581560.3133239047490.3539576330571.118071448220.5903421602981.52292287156-0.0501544899313-0.0582237528334-0.043969207603-0.0459736041581-0.1015195897580.3756805974510.166812050171-0.2857256921570.09698365254410.22990084225-0.001116242923250.002755407938220.180094336513-0.007543680170730.294371661895-18.7275179952-36.4409182932-32.4817698805
160.592657963241-0.256823560696-0.02451891604460.659200780944-0.1002600919590.5888602752560.05441407548970.2364169068250.000639557513978-0.202468576998-0.0837231306315-0.1339005837490.06779505872170.06744716933180.02481882813320.1594481390520.01976996392090.04616968698760.2314970238540.003774555837750.14639953169-5.05227123207-19.7698252745-49.9128752889
171.36461654741-0.397380072840.3958105310941.08709320972-0.2052362800640.9938340271310.1506783914350.299906784712-0.279595525594-0.353786892181-0.09388194172830.3379099213430.221983726333-0.125114096945-0.06244950547910.3297539511530.0322213138997-0.06062804867860.28154407416-0.07490379092810.316440166201-18.6809946405-40.6143134298-47.6139734939
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 88 )AA58 - 8858 - 88
33chain 'A' and (resid 89 through 159 )AA89 - 15989 - 159
44chain 'A' and (resid 160 through 228 )AA160 - 228160 - 228
55chain 'A' and (resid 229 through 285 )AA229 - 285229 - 285
66chain 'A' and (resid 286 through 331 )AA286 - 331286 - 331
77chain 'A' and (resid 332 through 456 )AA332 - 456332 - 456
88chain 'C' and (resid 1 through 57 )CJ1 - 571 - 57
99chain 'C' and (resid 58 through 285 )CJ58 - 28558 - 285
1010chain 'C' and (resid 286 through 456 )CJ286 - 456286 - 456
1111chain 'D' and (resid 1 through 47 )DQ1 - 471 - 47
1212chain 'D' and (resid 48 through 159 )DQ48 - 15948 - 159
1313chain 'D' and (resid 160 through 264 )DQ160 - 264160 - 264
1414chain 'D' and (resid 265 through 456 )DQ265 - 456265 - 456
1515chain 'B' and (resid 1 through 47 )BE1 - 471 - 47
1616chain 'B' and (resid 48 through 328 )BE48 - 32848 - 328
1717chain 'B' and (resid 329 through 456 )BE329 - 456329 - 456

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