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- PDB-2keq: Solution structure of DnaE intein from Nostoc punctiforme -

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Basic information

Entry
Database: PDB / ID: 2keq
TitleSolution structure of DnaE intein from Nostoc punctiforme
ComponentsDNA polymerase III alpha subunit, Nucleic acid binding OB-fold tRNA/helicase-type
KeywordsSPLICING / Intein / DnaE intein / Protein splicing / Protein trans splicing
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / helicase activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Hint domain superfamily / OB-fold nucleic acid binding domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA polymerase III, alpha subunit / Nucleic acid binding, OB-fold, tRNA/helicase-type
Similarity search - Component
Biological speciesNostoc punctiforme PCC 73102 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsOeemig, J.S. / Aranko, A.S. / Djupsj, J.B. / Iwai, H.
CitationJournal: Febs Lett. / Year: 2009
Title: Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification.
Authors: Oeemig, J.S. / Aranko, A.S. / Djupsjobacka, J. / Heinamaki, K. / Iwai, H.
History
DepositionFeb 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III alpha subunit, Nucleic acid binding OB-fold tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)15,9331
Polymers15,9331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA polymerase III alpha subunit, Nucleic acid binding OB-fold tRNA/helicase-type


Mass: 15932.979 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN OF N-INTEIN PART FROM DNA POLYMERASE III ALPHA SUBUNIT (RESIDUES 1-102) AND C-INTEIN PART FROM NUCLEIC ACID BINDING OB-FOLD, TRNA/HELICASE-TYPE (RESIDUES 103-137)
Source: (gene. exp.) Nostoc punctiforme PCC 73102 (bacteria)
Gene: DnaE, Npun_F4872 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: B2J066, UniProt: B2J821
Sequence detailsFUSION PROTEIN OF N-INTEIN PART FROM DNA POLYMERASE III ALPHA SUBUNIT (RESIDUES 1-102) AND C-INTEIN ...FUSION PROTEIN OF N-INTEIN PART FROM DNA POLYMERASE III ALPHA SUBUNIT (RESIDUES 1-102) AND C-INTEIN PART FROM NUCLEIC ACID BINDING OB-FOLD, TRNA/HELICASE-TYPE (RESIDUES 103-137)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1213D 1H-13C NOESY
NMR detailsText: 3D 1H-15N NOESY and 3D 1H-13C NOESY spectra were recorded with a mixing time of 80 and 70 msec, respectively.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] NpuDnaE-1, 10 mM sodium phosphate-2, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-20% 13C; U-99% 15N] NpuDnaE-3, 10 mM sodium phosphate-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMNpuDnaE-1[U-99% 13C; U-99% 15N]1
10 mMsodium phosphate-21
2 mMNpuDnaE-3[U-20% 13C; U-99% 15N]2
10 mMsodium phosphate-42
Sample conditionsIonic strength: 0.01 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3154 / NOE intraresidue total count: 712 / NOE long range total count: 1223 / NOE medium range total count: 433 / NOE sequential total count: 786
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.33 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0032 Å / Distance rms dev error: 0.0007 Å

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