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- PDB-1m3g: SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF MAPK PHOSPHATASE PA... -

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Entry
Database: PDB / ID: 1m3g
TitleSOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF MAPK PHOSPHATASE PAC-1: INSIGHTS INTO SUBSTRATE-INDUCED ENZYMATIC ACTIVATION
ComponentsDUAL SPECIFICITY PROTEIN PHOSPHATASE 2
KeywordsHYDROLASE / CATALYTIC DOMAIN / MAPK PHOSPHATASE / PAC-1
Function / homology
Function and homology information


: / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / peptidyl-threonine dephosphorylation / RAF-independent MAPK1/3 activation / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation ...: / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / peptidyl-threonine dephosphorylation / RAF-independent MAPK1/3 activation / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Negative regulation of MAPK pathway / nuclear membrane / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFarooq, A. / Zhou, M.-M.
CitationJournal: Structure / Year: 2003
Title: Solution Structure of the MAPK Phosphatase PAC-1 Catalytic Domain Insights into Substrate-Induced Enzymatic Activation of MKP
Authors: Farooq, A. / Plotnikova, O. / Chaturvedi, G. / Yan, S. / Zeng, L. / Zhang, Q. / Zhou, M.-M.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2003Provider: repository / Type: Initial release
SupersessionFeb 3, 2004ID: 1IKZ
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 2


Theoretical massNumber of molelcules
Total (without water)16,1291
Polymers16,1291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200
Representative

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Components

#1: Protein DUAL SPECIFICITY PROTEIN PHOSPHATASE 2 / MAPK Phosphatase PAC-1 / DUAL SPECIFICITY PROTEIN PHOSPHATASE PAC-1


Mass: 16129.417 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 170-314 / Mutation: C257S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: Q05923, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
131HNHA
141
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 0.5MM CATALYTIC DOMAIN MAPK PHOSPHATASE U-15N,13C; 5MM PHOSPHATE BUFFER PH 6.5
Sample conditionsIonic strength: 10 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
XPLOR/ARIABRUNGER (X-PLOR), NILGES, O'DONOGHUE (ARIA)structure solution
XwinNMRcollection
NMRPipeprocessing
NMRViewdata analysis
XPLOR/ARIABRUNGER (X-PLOR)/ NILGES, O'DONOGHUE (ARIA)refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 1

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