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

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Basic information

Entry
Database: PDB / ID: 5udr
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN
ComponentsATP-utilizing enzyme of the PP-loopsuperfamily
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase
Function / homology
Function and homology information


intrinsic cysteine-dependent pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / sulfurtransferase activity / NAD+ synthase (glutamine-hydrolyzing) 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
: / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / ATP-dependent sacrificial sulfur transferase LarE / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 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 / Structure summary / Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-utilizing enzyme of the PP-loopsuperfamily
B: ATP-utilizing enzyme of the PP-loopsuperfamily
C: ATP-utilizing enzyme of the PP-loopsuperfamily
D: ATP-utilizing enzyme of the PP-loopsuperfamily
E: ATP-utilizing enzyme of the PP-loopsuperfamily
F: ATP-utilizing enzyme of the PP-loopsuperfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,43414
Polymers190,3136
Non-polymers2,1218
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-109 kcal/mol
Surface area61920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.095, 108.095, 324.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
ATP-utilizing enzyme of the PP-loopsuperfamily / PP-loop superfamily ATP-binding protein / TIGR00268 family protein / Uncharacterized protein


Mass: 31718.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria)
Gene: A8P51_04975, IV39_GL000116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452
Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: Chemical
ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H16N2O8P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.49 Å3/Da / Density % sol: 50.68 % / Mosaicity: 0.14 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 ul 23 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) was mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 ...Details: 5 ul 23 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) was mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 150 mM ammonium sulfate. Crystals grew to full size within 4 days and remained in the drop for 4 months without notable changes. A single crystal was then transfered to a 10 ul drop containing ~100 mM beta-nicotinamide mononucleotide, 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH) and 50 mM BIS-TRIS pH 6.5. The drop was incubated for 11 days over a hanging drop reservoir containing 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate before being directly frozen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.62→48.42 Å / Num. obs: 59143 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 21.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.62-2.6912.11.2860.72199
11.41-48.428.90.0320.999198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.59 Å48.42 Å
Translation7.59 Å48.42 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→48.42 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2465 5358 4.84 %
Rwork0.2155 --
obs0.217 110671 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.94 Å2 / Biso mean: 61.9946 Å2 / Biso min: 28.19 Å2
Refinement stepCycle: final / Resolution: 2.62→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11121 0 134 136 11391
Biso mean--87.33 51.5 -
Num. residues----1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611442
X-RAY DIFFRACTIONf_angle_d0.73315538
X-RAY DIFFRACTIONf_chiral_restr0.0491823
X-RAY DIFFRACTIONf_plane_restr0.0052020
X-RAY DIFFRACTIONf_dihedral_angle_d14.9443915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6182-2.6480.39491610.33463460362197
2.648-2.67910.31451840.31334943678100
2.6791-2.71180.31321570.294535393696100
2.7118-2.74610.36891860.290134943680100
2.7461-2.78230.31811800.281435473727100
2.7823-2.82040.27071560.278634833639100
2.8204-2.86070.31811930.269435123705100
2.8607-2.90330.29661520.259935433695100
2.9033-2.94870.30951970.262335253722100
2.9487-2.9970.30471690.267835383707100
2.997-3.04870.32231940.274934633657100
3.0487-3.10410.32711740.272335293703100
3.1041-3.16380.28482350.265734773712100
3.1638-3.22840.31842060.266934593665100
3.2284-3.29860.27771520.247635473699100
3.2986-3.37530.28641420.238135493691100
3.3753-3.45970.27011730.221735443717100
3.4597-3.55320.24091760.226635033679100
3.5532-3.65770.24992460.219234333679100
3.6577-3.77570.27221990.214635013700100
3.7757-3.91060.24332020.204934883690100
3.9106-4.06710.20391680.195235053673100
4.0671-4.25210.21671450.183935693714100
4.2521-4.47620.16831750.169635353710100
4.4762-4.75640.21631920.172734853677100
4.7564-5.12330.20751770.179935403717100
5.1233-5.63810.24631600.201335233683100
5.6381-6.45240.27841620.219935203682100
6.4524-8.12310.20541520.194335423694100
8.1231-48.43070.19321930.18123466365999

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