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

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Basic information

Entry
Database: PDB / ID: 6utt
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with calcium
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
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: 2.49 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)191,53920
Polymers190,3136
Non-polymers1,22614
Water1,56787
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 area16320 Å2
ΔGint-228 kcal/mol
Surface area62230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.661, 107.661, 320.418
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 3 through 6 or (resid 7...
21(chain B and (resid 3 through 6 or (resid 7...
31(chain C and (resid 3 through 6 or (resid 7...
41(chain D and (resid 3 through 18 or resid 20...
51(chain E and (resid 3 through 6 or (resid 7...
61(chain F and (resid 3 through 6 or (resid 7...

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
11THRTHRTHRTHR(chain A and (resid 3 through 6 or (resid 7...AA3 - 63 - 6
12LYSLYSLYSLYS(chain A and (resid 3 through 6 or (resid 7...AA77
13ALAALAALAALA(chain A and (resid 3 through 6 or (resid 7...AA2 - 2762 - 276
14ALAALAALAALA(chain A and (resid 3 through 6 or (resid 7...AA2 - 2762 - 276
15ALAALAALAALA(chain A and (resid 3 through 6 or (resid 7...AA2 - 2762 - 276
16ALAALAALAALA(chain A and (resid 3 through 6 or (resid 7...AA2 - 2762 - 276
21THRTHRTHRTHR(chain B and (resid 3 through 6 or (resid 7...BB3 - 63 - 6
22LYSLYSLYSLYS(chain B and (resid 3 through 6 or (resid 7...BB77
23ALAALAARGARG(chain B and (resid 3 through 6 or (resid 7...BB2 - 2592 - 259
24ALAALAARGARG(chain B and (resid 3 through 6 or (resid 7...BB2 - 2592 - 259
25ALAALAARGARG(chain B and (resid 3 through 6 or (resid 7...BB2 - 2592 - 259
26ALAALAARGARG(chain B and (resid 3 through 6 or (resid 7...BB2 - 2592 - 259
31THRTHRTHRTHR(chain C and (resid 3 through 6 or (resid 7...CC3 - 63 - 6
32LYSLYSLYSLYS(chain C and (resid 3 through 6 or (resid 7...CC77
33ALAALAARGARG(chain C and (resid 3 through 6 or (resid 7...CC2 - 2592 - 259
41THRTHRLEULEU(chain D and (resid 3 through 18 or resid 20...DD3 - 183 - 18
42ARGARGGLUGLU(chain D and (resid 3 through 18 or resid 20...DD20 - 6020 - 60
43GLUGLUGLUGLU(chain D and (resid 3 through 18 or resid 20...DD6161
44THRTHRARGARG(chain D and (resid 3 through 18 or resid 20...DD3 - 2593 - 259
45THRTHRARGARG(chain D and (resid 3 through 18 or resid 20...DD3 - 2593 - 259
46THRTHRARGARG(chain D and (resid 3 through 18 or resid 20...DD3 - 2593 - 259
47THRTHRARGARG(chain D and (resid 3 through 18 or resid 20...DD3 - 2593 - 259
51THRTHRTHRTHR(chain E and (resid 3 through 6 or (resid 7...EE3 - 63 - 6
52LYSLYSLYSLYS(chain E and (resid 3 through 6 or (resid 7...EE77
53ALAALATRPTRP(chain E and (resid 3 through 6 or (resid 7...EE2 - 2792 - 279
54ALAALATRPTRP(chain E and (resid 3 through 6 or (resid 7...EE2 - 2792 - 279
55ALAALATRPTRP(chain E and (resid 3 through 6 or (resid 7...EE2 - 2792 - 279
56ALAALATRPTRP(chain E and (resid 3 through 6 or (resid 7...EE2 - 2792 - 279
61THRTHRTHRTHR(chain F and (resid 3 through 6 or (resid 7...FF3 - 63 - 6
62LYSLYSLYSLYS(chain F and (resid 3 through 6 or (resid 7...FF77
63ALAALASERSER(chain F and (resid 3 through 6 or (resid 7...FF2 - 2602 - 260
64ALAALASERSER(chain F and (resid 3 through 6 or (resid 7...FF2 - 2602 - 260
65ALAALASERSER(chain F and (resid 3 through 6 or (resid 7...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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.44 Å3/Da / Density % sol: 49.58 % / Mosaicity: 0.12 °
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 calcium chloride, 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: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→48.15 Å / Num. obs: 66185 / % possible obs: 98.5 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Rrim(I) all: 0.079 / Net I/σ(I): 18.2
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
2.49-2.558.20.9173131238340.7580.3280.976286.6
11.67-48.156.80.02249767370.9990.0090.02450.195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.55 Å48.15 Å
Translation7.55 Å48.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 2.49→38.49 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2559 6194 5 %
Rwork0.2016 --
obs0.2043 66094 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.63 Å2 / Biso mean: 66.8504 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.49→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11462 0 62 87 11611
Biso mean--66.64 54.42 -
Num. residues----1505
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6143X-RAY DIFFRACTION12.007TORSIONAL
12B6143X-RAY DIFFRACTION12.007TORSIONAL
13C6143X-RAY DIFFRACTION12.007TORSIONAL
14D6143X-RAY DIFFRACTION12.007TORSIONAL
15E6143X-RAY DIFFRACTION12.007TORSIONAL
16F6143X-RAY DIFFRACTION12.007TORSIONAL
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 (%)
2.49-2.520.35721450.31692758290369
2.52-2.550.38382070.290839964203100
2.55-2.580.38612120.290640064218100
2.58-2.610.36471930.284140024195100
2.61-2.640.32952490.276339954244100
2.64-2.680.3361970.280740084205100
2.68-2.720.33482060.263939834189100
2.72-2.760.32951770.268140584235100
2.76-2.80.31542250.260839324157100
2.8-2.850.34812320.261140074239100
2.85-2.90.30952220.248539664188100
2.9-2.950.33652180.24643940415899
2.95-3.010.30862120.25273977418999
3.01-3.070.3121930.2473804399795
3.07-3.130.29872050.24913959416499
3.13-3.210.31331970.253239984195100
3.21-3.290.30632330.24839894222100
3.29-3.380.31282070.241440364243100
3.38-3.480.30481950.225139824177100
3.48-3.590.28882310.21843949418099
3.59-3.720.30342200.20573956417699
3.72-3.860.20952250.18913935416099
3.86-4.040.26411890.17633964415399
4.04-4.250.2272030.16723985418899
4.25-4.520.18851810.16173927410898
4.52-4.870.19091950.1553955415098
4.87-5.350.18382300.16193918414898
5.36-6.130.22522170.18313701391893
6.13-7.710.2362140.182740054219100
7.71-38.490.19131640.15963933409797

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