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- PDB-2sns: STAPHYLOCOCCAL NUCLEASE. PROPOSED MECHANISM OF ACTION BASED ON ST... -

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Entry
Database: PDB / ID: 2sns
TitleSTAPHYLOCOCCAL NUCLEASE. PROPOSED MECHANISM OF ACTION BASED ON STRUCTURE OF ENZYME-THYMIDINE 3(PRIME),5(PRIME)-BIPHOSPHATE-CALCIUM ION COMPLEX AT 1.5-ANGSTROMS RESOLUTION
ComponentsTHERMONUCLEASE PRECURSOR
KeywordsHYDROLASE (PHOSPHORIC DIESTER)
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsLegg, M.J. / Cotton, F.A. / Hazen Jr., E.E.
Citation
Journal: Thesis, Texas Agricultural and Mechanical University
Year: 1977
Authors: Cotton, F.A. / Hazen Jr., E.E. / Legg, M.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3',5'-bisphosphate-calcium ion complex at 1.5-A resolution.
Authors: Cotton, F.A. / Hazenjunior, E.E. / Legg, M.J.
#3: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: The Nucleotide Binding Site of Staphylococcal Nuclease and a New Approach to the Refinement of the Crystal Structures of Biological Macromolecules
Authors: Collins, D.M. / Cotton, F.A. / Hazenjunior, E.E. / Legg, M.J.
#4: Journal: J.Am.Chem.Soc. / Year: 1974
Title: Structure of Bis (Methylguanidinium) Monohydrogen Orthophosphate,A Model for the Arginine-Phosphate Interactions at the Active Site of Staphylococcal Nuclease and Other Phosphohydrolytic Enzymes
Authors: Cotton, F.A. / Day, V.W. / Hazenjunior, E.E. / Larsen, S. / Wong, S.T.K.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Some Aspects of the Structure of Staphylococcal Nuclease,Part I,Crystallographic Studies
Authors: Cotton, F.A. / Bier, C.J. / Day, V.W. / Hazenjunior, E.E. / Larsen, S.
#6: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Some Aspects of the Structure of Staphylococcal Nuclease,Part II,Studies in Solution
Authors: Anfinsen, C.B. / Schechter, A.N. / Taniuchi, H.
#7: Journal: J.Biol.Chem. / Year: 1971
Title: A High Resolution Structure of an Inhibitor Complex of the Extracellular Nuclease of Staphylococcus Aureus,I.Experimental Procedures and Chain Tracing
Authors: Arnone, A. / Bier, C.J. / Cotton, F.A. / Day, V.W. / Hazenjunior, E.E. / Richardson, D.C. / Richardson, J.S. / Yonath, A.
#8: Journal: The Enzymes,Third Edition / Year: 1971
Title: Staphylococcal Nuclease X-Ray Structure
Authors: Cotton, F.A. / Hazenjunior, E.E.
#2: Journal: Thesis, Texas Agricultural and Mechanical University
Year: 1976
Authors: Stanislowski, A.G.
#9: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMay 14, 1982Processing site: BNL
SupersessionJul 29, 1982ID: 1SNS
Revision 1.0Jul 29, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET THERE ARE TWO BETA SHEETS WHICH FORM A DISTORTED VERSION OF A 5-STRANDED BETA BARREL. THE ...SHEET THERE ARE TWO BETA SHEETS WHICH FORM A DISTORTED VERSION OF A 5-STRANDED BETA BARREL. THE BARREL PATTERN IS -1,-1,+3, +1 IN THE NOTATION OF RICHARDSON.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THERMONUCLEASE PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2853
Polymers16,8421
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.190, 48.190, 63.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: SEE REMARK 6.

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Components

#1: Protein THERMONUCLEASE PRECURSOR


Mass: 16842.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
Compound detailsTHE ENZYME IS INACTIVE IN THE PRESENCE OF A CALCIUM ION AND THE MOLECULE THYMIDINE 3(PRIME)-5(PRIME) ...THE ENZYME IS INACTIVE IN THE PRESENCE OF A CALCIUM ION AND THE MOLECULE THYMIDINE 3(PRIME)-5(PRIME) DIPHOSPHATE. THE STRUCTURE REPORTED HERE IS THE STRUCTURE WITH CALCIUM ION AND INHIBITOR BOUND.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 18400 / Num. measured all: 25000

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Processing

RefinementHighest resolution: 1.5 Å
Details: THE ELECTRON DENSITY MAP DID NOT DISTINCTLY REVEAL THE LOCATION OF THE FIRST FIVE OR THE LAST EIGHT AMINO ACID RESIDUES (I.E. 1-5 AND 142-149). THE FIRST FIVE RESIDUES COULD BE FITTED TO THE ...Details: THE ELECTRON DENSITY MAP DID NOT DISTINCTLY REVEAL THE LOCATION OF THE FIRST FIVE OR THE LAST EIGHT AMINO ACID RESIDUES (I.E. 1-5 AND 142-149). THE FIRST FIVE RESIDUES COULD BE FITTED TO THE WEAK DENSITY IN SEVERAL DIFFERENT CONFORMATIONS, BUT THERE WAS INSUFFICIENT DENSITY NEAR THE CARBOXY TERMINUS TO PERMIT ANY ATTEMPTS AT FITTING. ATOMIC COORDINATES FOR ALL FITTED ATOMS APPEAR IN THIS ENTRY.
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 26 0 1151
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5

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