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- PDB-6utr: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 6utr
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with copper
ComponentsATP-dependent sacrificial sulfur transferase LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / PP-loop / ATP pyrophophatase domain / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolyzing) activity / 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
COPPER (II) ION / PHOSPHATE ION / Lactate racemization operon protein LarE / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsFellner, M. / Huizenga, K. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Sci Rep / Year: 2020
Title: Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.
Authors: Fellner, M. / Huizenga, K.G. / Hausinger, R.P. / Hu, J.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent sacrificial sulfur transferase LarE
B: ATP-dependent sacrificial sulfur transferase LarE
C: ATP-dependent sacrificial sulfur transferase LarE
D: ATP-dependent sacrificial sulfur transferase LarE
E: ATP-dependent sacrificial sulfur transferase LarE
F: ATP-dependent sacrificial sulfur transferase LarE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,49019
Polymers190,3136
Non-polymers1,17713
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration is a hexamer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-206 kcal/mol
Surface area63250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.978, 108.978, 323.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 through 21 and (name N...
21(chain B and ((resid 8 through 21 and (name N...
31(chain C and ((resid 8 through 21 and (name N...
41(chain D and (resid 8 through 43 or (resid 44...
51(chain E and ((resid 8 through 21 and (name N...
61(chain F and ((resid 8 through 21 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVAL(chain A and ((resid 8 through 21 and (name N...AA8 - 218 - 21
12ALAALAALAALA(chain A and ((resid 8 through 21 and (name N...AA2 - 2762 - 276
13ALAALAALAALA(chain A and ((resid 8 through 21 and (name N...AA2 - 2762 - 276
14ALAALAALAALA(chain A and ((resid 8 through 21 and (name N...AA2 - 2762 - 276
15ALAALAALAALA(chain A and ((resid 8 through 21 and (name N...AA2 - 2762 - 276
21LYSLYSVALVAL(chain B and ((resid 8 through 21 and (name N...BB8 - 218 - 21
22ALAALAARGARG(chain B and ((resid 8 through 21 and (name N...BB2 - 2592 - 259
23ALAALAARGARG(chain B and ((resid 8 through 21 and (name N...BB2 - 2592 - 259
24ALAALAARGARG(chain B and ((resid 8 through 21 and (name N...BB2 - 2592 - 259
25ALAALAARGARG(chain B and ((resid 8 through 21 and (name N...BB2 - 2592 - 259
31LYSLYSVALVAL(chain C and ((resid 8 through 21 and (name N...CC8 - 218 - 21
32ALAALAARGARG(chain C and ((resid 8 through 21 and (name N...CC2 - 2592 - 259
33ALAALAARGARG(chain C and ((resid 8 through 21 and (name N...CC2 - 2592 - 259
34ALAALAARGARG(chain C and ((resid 8 through 21 and (name N...CC2 - 2592 - 259
35ALAALAARGARG(chain C and ((resid 8 through 21 and (name N...CC2 - 2592 - 259
41LYSLYSGLYGLY(chain D and (resid 8 through 43 or (resid 44...DD8 - 438 - 43
42ARGARGARGARG(chain D and (resid 8 through 43 or (resid 44...DD4444
43LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
44LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
45LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
46LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
47LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
48LYSLYSARGARG(chain D and (resid 8 through 43 or (resid 44...DD8 - 2598 - 259
51LYSLYSVALVAL(chain E and ((resid 8 through 21 and (name N...EE8 - 218 - 21
52ALAALATRPTRP(chain E and ((resid 8 through 21 and (name N...EE2 - 2792 - 279
53ALAALATRPTRP(chain E and ((resid 8 through 21 and (name N...EE2 - 2792 - 279
54ALAALATRPTRP(chain E and ((resid 8 through 21 and (name N...EE2 - 2792 - 279
55ALAALATRPTRP(chain E and ((resid 8 through 21 and (name N...EE2 - 2792 - 279
61LYSLYSVALVAL(chain F and ((resid 8 through 21 and (name N...FF8 - 218 - 21
62ALAALASERSER(chain F and ((resid 8 through 21 and (name N...FF2 - 2602 - 260
63ALAALASERSER(chain F and ((resid 8 through 21 and (name N...FF2 - 2602 - 260
64ALAALASERSER(chain F and ((resid 8 through 21 and (name N...FF2 - 2602 - 260
65ALAALASERSER(chain F and ((resid 8 through 21 and (name N...FF2 - 2602 - 260

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Components

#1: Protein
ATP-dependent sacrificial sulfur transferase LarE / ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop ...ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop superfamily ATP-binding protein / TIGR00268 family protein


Mass: 31718.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria)
Gene: larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302
Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.29 % / Mosaicity: 0.18 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 uL ~25 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 5 uL of reservoir solution. Hanging drop reservoir contained 100 uL of 30% v/v pentaerythritol ethoxylate (15/4 EO/OH), ...Details: 5 uL ~25 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 5 uL of reservoir solution. Hanging drop reservoir contained 100 uL of 30% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate. Crystal soaked 60 minutes in 3.8 mM copper(II) sulfate, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.41→48.74 Å / Num. obs: 75724 / % possible obs: 99.5 % / Redundancy: 15.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.028 / Rrim(I) all: 0.111 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.41-2.4614.91.2876094740950.7050.3391.3321.993.1
12.07-48.74130.05695777360.9990.0150.05835.698.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.61 Å48.74 Å
Translation7.61 Å48.74 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PHENIX1.17-3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 2.41→48.35 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 27.16
RfactorNum. reflection% reflection
Rfree0.2536 7160 5.03 %
Rwork0.2081 --
obs0.2103 75618 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.14 Å2 / Biso mean: 66.4115 Å2 / Biso min: 27.52 Å2
Refinement stepCycle: final / Resolution: 2.41→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11401 0 57 122 11580
Biso mean--64.47 54.14 -
Num. residues----1498
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6011X-RAY DIFFRACTION12.564TORSIONAL
12B6011X-RAY DIFFRACTION12.564TORSIONAL
13C6011X-RAY DIFFRACTION12.564TORSIONAL
14D6011X-RAY DIFFRACTION12.564TORSIONAL
15E6011X-RAY DIFFRACTION12.564TORSIONAL
16F6011X-RAY DIFFRACTION12.564TORSIONAL
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 (%)
2.41-2.440.38432480.33673842409086
2.44-2.470.37872780.30845124790100
2.47-2.50.31112190.302345074726100
2.5-2.530.34672480.286546114859100
2.53-2.560.32312470.275644684715100
2.56-2.60.34492470.276645614808100
2.6-2.640.33082460.272844644710100
2.64-2.680.31652730.268145234796100
2.68-2.720.34232270.27245614788100
2.72-2.760.34342320.265745034735100
2.76-2.810.34022850.268545204805100
2.81-2.860.27312660.242244944760100
2.86-2.920.28312050.23364543474899
2.92-2.980.30462170.23645524769100
2.98-3.040.30672550.237645144769100
3.04-3.110.3162120.250245844796100
3.11-3.190.3152270.248245264753100
3.19-3.280.31371980.257745594757100
3.28-3.370.30282340.235445354769100
3.37-3.480.28362830.222645334816100
3.48-3.60.25612770.217344674744100
3.6-3.750.26861880.210946354823100
3.75-3.920.2561890.202645534742100
3.92-4.130.23352180.187145254743100
4.13-4.380.21582450.178945444789100
4.39-4.720.18992060.16545834789100
4.72-5.20.19832720.167645124784100
5.2-5.950.25812430.1884462470599
5.95-7.490.21882380.192245384776100
7.49-48.350.1792370.16334519475699

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