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- PDB-5udt: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 5udt
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with AMP
ComponentsLactate racemization operon protein LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / AMP / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / sulfurtransferase activity / lyase activity / ATP binding
Similarity search - Function
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.188 Å
AuthorsFellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Authors: Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionDec 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactate racemization operon protein LarE
B: Lactate racemization operon protein LarE
C: Lactate racemization operon protein LarE
D: Lactate racemization operon protein LarE
E: Lactate racemization operon protein LarE
F: Lactate racemization operon protein LarE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,92415
Polymers190,3136
Non-polymers1,6119
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-93 kcal/mol
Surface area62080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.299, 166.299, 124.925
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 17 and (name N...
21(chain B and ((resid 4 through 17 and (name N...
31(chain C and ((resid 4 through 17 and (name N...
41(chain E and ((resid 4 through 17 and (name N...
12(chain D and ((resid 26 through 42 and (name N...
22(chain F and ((resid 26 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUASPASP(chain A and ((resid 4 through 17 and (name N...AA4 - 174 - 17
121THRTHRPHEPHE(chain A and ((resid 4 through 17 and (name N...AA3 - 2583 - 258
131THRTHRPHEPHE(chain A and ((resid 4 through 17 and (name N...AA3 - 2583 - 258
141THRTHRPHEPHE(chain A and ((resid 4 through 17 and (name N...AA3 - 2583 - 258
151THRTHRPHEPHE(chain A and ((resid 4 through 17 and (name N...AA3 - 2583 - 258
211LEULEUASPASP(chain B and ((resid 4 through 17 and (name N...BB4 - 174 - 17
221ALAALAARGARG(chain B and ((resid 4 through 17 and (name N...BB2 - 2592 - 259
231ALAALAARGARG(chain B and ((resid 4 through 17 and (name N...BB2 - 2592 - 259
241ALAALAARGARG(chain B and ((resid 4 through 17 and (name N...BB2 - 2592 - 259
251ALAALAARGARG(chain B and ((resid 4 through 17 and (name N...BB2 - 2592 - 259
311LEULEUASPASP(chain C and ((resid 4 through 17 and (name N...CC4 - 174 - 17
321THRTHRPHEPHE(chain C and ((resid 4 through 17 and (name N...CC3 - 2583 - 258
331THRTHRPHEPHE(chain C and ((resid 4 through 17 and (name N...CC3 - 2583 - 258
341THRTHRPHEPHE(chain C and ((resid 4 through 17 and (name N...CC3 - 2583 - 258
351THRTHRPHEPHE(chain C and ((resid 4 through 17 and (name N...CC3 - 2583 - 258
411LEULEUASPASP(chain E and ((resid 4 through 17 and (name N...EE4 - 174 - 17
421LEULEUPHEPHE(chain E and ((resid 4 through 17 and (name N...EE4 - 2584 - 258
431LEULEUPHEPHE(chain E and ((resid 4 through 17 and (name N...EE4 - 2584 - 258
441LEULEUPHEPHE(chain E and ((resid 4 through 17 and (name N...EE4 - 2584 - 258
451LEULEUPHEPHE(chain E and ((resid 4 through 17 and (name N...EE4 - 2584 - 258
112SERSERLEULEU(chain D and ((resid 26 through 42 and (name N...DD26 - 4226 - 42
122SERSERSERSER(chain D and ((resid 26 through 42 and (name N...DD26 - 26026 - 260
132SERSERSERSER(chain D and ((resid 26 through 42 and (name N...DD26 - 26026 - 260
142SERSERSERSER(chain D and ((resid 26 through 42 and (name N...DD26 - 26026 - 260
152SERSERSERSER(chain D and ((resid 26 through 42 and (name N...DD26 - 26026 - 260
212SERSERSERSER(chain F and ((resid 26 and (name N or name...FF2626
222VALVALPHEPHE(chain F and ((resid 26 and (name N or name...FF23 - 25823 - 258
232VALVALPHEPHE(chain F and ((resid 26 and (name N or name...FF23 - 25823 - 258
242VALVALPHEPHE(chain F and ((resid 26 and (name N or name...FF23 - 25823 - 258
252VALVALPHEPHE(chain F and ((resid 26 and (name N or name...FF23 - 25823 - 258

NCS ensembles :
ID
1
2

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Components

#1: Protein
Lactate racemization operon protein LarE


Mass: 31718.766 Da / Num. of mol.: 6 / Mutation: C-terminal fusion to ASWSHPQFEK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larE, lp_0109 / Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: F9UST4
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

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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: 2.62 Å3/Da / Density % sol: 53.06 % / Mosaicity: 0.23 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 ul ~21 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl, 4 mM adenosine triphosphate, 10 mM magnesium chloride) mixed with 2 ul reservoir solution. Hanging drop reservoir contained 100 ul ...Details: 4 ul ~21 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl, 4 mM adenosine triphosphate, 10 mM magnesium chloride) mixed with 2 ul reservoir solution. Hanging drop reservoir contained 100 ul of 28% Tacsimate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.188→47.185 Å / Num. obs: 33575 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 81.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.19-3.345.30.6380.764199.1
10.57-47.184.60.0210.999197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.35 Å47.18 Å
Translation8.35 Å47.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 3.188→47.185 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.1
RfactorNum. reflection% reflection
Rfree0.2727 3291 5.12 %
Rwork0.2068 --
obs0.2102 32111 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.3 Å2 / Biso mean: 90.614 Å2 / Biso min: 38.75 Å2
Refinement stepCycle: final / Resolution: 3.188→47.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9876 0 99 0 9975
Biso mean--92.66 --
Num. residues----1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110163
X-RAY DIFFRACTIONf_angle_d1.11513858
X-RAY DIFFRACTIONf_chiral_restr0.0611619
X-RAY DIFFRACTIONf_plane_restr0.011821
X-RAY DIFFRACTIONf_dihedral_angle_d14.4733299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3830X-RAY DIFFRACTION10.828TORSIONAL
12B3830X-RAY DIFFRACTION10.828TORSIONAL
13C3830X-RAY DIFFRACTION10.828TORSIONAL
14E3830X-RAY DIFFRACTION10.828TORSIONAL
21D1270X-RAY DIFFRACTION10.828TORSIONAL
22F1270X-RAY DIFFRACTION10.828TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1879-3.23340.34541060.31492478258496
3.2334-3.28160.34941400.305825362676100
3.2816-3.33290.40531220.292925782700100
3.3329-3.38750.37261380.288525592697100
3.3875-3.44590.34661560.268424922648100
3.4459-3.50860.35241470.27332496264399
3.5086-3.5760.29951480.253325602708100
3.576-3.6490.34911430.26425382681100
3.649-3.72830.38811360.267625082644100
3.7283-3.8150.31781260.231825522678100
3.815-3.91040.25831370.201425602697100
3.9104-4.0160.26291320.194125802712100
4.016-4.13410.23811560.187825082664100
4.1341-4.26750.25971380.183625582696100
4.2675-4.41990.28761360.196425412677100
4.4199-4.59670.27271300.179125462676100
4.5967-4.80580.25711500.178625342684100
4.8058-5.05880.25011580.167725552713100
5.0588-5.37540.24571500.172625212671100
5.3754-5.78970.26141400.187225422682100
5.7897-6.37110.2261260.199225542680100
6.3711-7.29010.28671130.209425712684100
7.2901-9.17370.23431120.170525712683100
9.1737-47.18980.21741510.19182493264498
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)
16.34523.05114.83150.93164.146-0.646-0.91891.04640.337-0.57860.4512-1.41170.09851.0242.4941-0.25490.49811.0409-0.09020.79947.3585-21.3468-27.602
24.8387-1.609-2.11758.38762.35924.9551-0.0994-0.77290.49170.11890.49880.9445-0.22581.2123-0.41960.78520.0460.22271.33430.26380.80440.9044-37.5024-37.314
32.50632.48312.6657.44440.62973.5274-0.07670.37870.24940.08380.36840.3688-0.41891.6709-0.14351.3334-0.01760.28391.72760.30610.742652.9885-26.0871-36.0795
40.0131-0.640.99914.5674-0.45042.86630.45950.07370.40190.4942-0.354-0.0443-0.3387-0.7727-0.12670.942-0.03410.22441.49080.25680.659450.1436-48.4909-33.285
56.88372.259-4.28457.4661-3.85313.38290.01920.03170.17550.10540.12840.09250.1636-0.3095-0.15660.7796-0.01810.00860.97690.03090.228557.8589-61.5951-34.4659
65.2371-4.29521.25959.334-3.46824.2270.43770.46470.4032-0.4211-0.21720.38580.1115-0.3994-0.20430.505-0.1666-0.02780.96510.04170.381548.2798-39.20233.5005
72.24590.58130.14689.56120.7438-0.09330.0225-0.1532-0.01380.90860.02380.43290.14380.123-0.06620.7497-0.14720.03881.02780.01980.278652.6119-54.206610.2756
84.5362-0.6846-0.29659.091-2.35787.60470.50010.556-0.5924-1.0678-0.0720.8160.1975-1.0866-0.30730.7414-0.0407-0.16011.4298-0.14710.585843.1384-45.526-0.6196
90.3572-1.6923-0.36824.72541.22840.10270.51920.3540.1694-1.0967-0.80010.46670.27720.3730.37291.0864-0.10440.00211.2634-0.0130.43256.6666-57.0805-0.6314
104.2719-0.9793-0.7024.3357-0.37595.0909-0.086-0.5162-0.07420.14620.16510.03910.2351-0.4842-0.06180.9149-0.1682-0.040.8642-0.00440.217667.1242-67.6982-5.9432
117.3427-3.2755-2.20824.92171.3321.608-0.0545-0.2645-0.4217-0.31880.09150.56020.0814-0.0638-0.0520.8221-0.0757-0.07990.79910.07770.304279.3672-26.1498-9.6878
127.30552.92020.76256.2563-0.39052.99580.07750.23960.00440.16080.1308-0.0622-0.46740.0691-0.20760.7210.0482-0.00930.5621-0.02570.163985.6092-50.0028-25.3308
134.2541.2764-4.46977.9421-0.16916.8542-0.00061.1666-1.1678-2.2962-1.6935-0.0529-1.9594-0.96131.74812.03030.1022-0.23321.1613-0.23861.288275.1378-106.4561-27.9192
143.8728-0.7762-2.28525.38970.17761.27910.0753-0.8756-1.0367-0.09350.0846-0.6312-0.18570.3598-0.30311.2131-0.2162-0.22711.09890.1511.051775.4533-105.1693-17.8626
157.75650.34690.40186.1968-0.28373.89150.2913-0.4335-0.49390.51060.1361-0.04150.2582-0.0455-0.4180.8566-0.2548-0.10560.74150.04140.305264.2813-83.6675-15.811
162.3917-2.2972-0.88869.71044.43273.7697-0.04870.8776-0.7497-0.5986-0.01640.6798-0.4071-0.10970.04740.58920.0745-0.02461.2411-0.07820.5677106.2424-84.8228-37.6178
177.03690.91310.36235.5013-0.8681.63550.0261-0.0619-0.11580.28070.1725-0.06010.2405-0.1302-0.15190.73140.0614-0.02480.64060.02420.173591.2956-67.7107-21.5215
184.3558-1.6463-0.26164.40970.85741.68030.31210.9462-2.0889-0.8420.1328-0.292-0.19910.2886-0.42631.0106-0.3549-0.01861.8425-0.60131.422469.0497-88.5219-60.8384
195.8063-1.1295-0.41064.6919-1.20986.3551-0.24190.2755-0.329-0.30080.16160.0970.1721-0.81240.07680.8286-0.12910.07440.8437-0.09780.24969.3359-67.6969-44.1239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 42 )A3 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 114 )A43 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 162 )A115 - 162
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 206 )A163 - 206
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 258 )A207 - 258
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 58 )B2 - 58
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 114 )B59 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 162 )B115 - 162
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 189 )B163 - 189
10X-RAY DIFFRACTION10chain 'B' and (resid 190 through 259 )B190 - 259
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 177 )C3 - 177
12X-RAY DIFFRACTION12chain 'C' and (resid 178 through 258 )C178 - 258
13X-RAY DIFFRACTION13chain 'D' and (resid 26 through 72 )D26 - 72
14X-RAY DIFFRACTION14chain 'D' and (resid 73 through 177 )D73 - 177
15X-RAY DIFFRACTION15chain 'D' and (resid 178 through 260 )D178 - 260
16X-RAY DIFFRACTION16chain 'E' and (resid 4 through 189 )E4 - 189
17X-RAY DIFFRACTION17chain 'E' and (resid 190 through 258 )E190 - 258
18X-RAY DIFFRACTION18chain 'F' and (resid 23 through 189 )F23 - 189
19X-RAY DIFFRACTION19chain 'F' and (resid 190 through 258 )F190 - 258

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