6IHU

Crystal structure of bacterial serine phosphatase bearing R161A mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insight into the Mechanism of Staphylococcus aureus Stp1 Phosphatase.

Yang, T.Liu, T.Gan, J.Yu, K.Chen, K.Xue, W.Lan, L.Yang, S.Yang, C.G.

(2019) ACS Infect Dis 5: 841-850

  • DOI: 10.1021/acsinfecdis.8b00316
  • Primary Citation of Related Structures:  
    6IHR, 6IHT, 6IHS, 6IHL, 6IHV, 6IHU, 6IHW

  • PubMed Abstract: 
  • Staphylococcus aureus Stp1, which belongs to the bacterial metal-dependent protein phosphatase (PPM) family, is a promising candidate for antivirulence targeting. How Stp1 recognizes the phosphorylated peptide remains unclear, however. In order to investigate the recognition mechanism of Stp1 in depth, we have determined a series of crystal structures of S ...

    Staphylococcus aureus Stp1, which belongs to the bacterial metal-dependent protein phosphatase (PPM) family, is a promising candidate for antivirulence targeting. How Stp1 recognizes the phosphorylated peptide remains unclear, however. In order to investigate the recognition mechanism of Stp1 in depth, we have determined a series of crystal structures of S. aureus Stp1 in different states and the structural complex of Stp1 bound with a phosphorylated peptide His12. Different phosphorylated peptides, including MgrA- and GraR-derived phosphopeptides, are substrates of Stp1, which supports the function of Stp1 as a selective Ser/Thr phosphatase. In addition, interestingly, the crystal structures of R161-Stp1 variants combined with the biochemical activity validations have uncovered that R161 residue plays a key role to control the conformation switches of the flap domain in order to facilitate substrate binding and the dephosphorylation process. Our findings provide crucial structural insight into the molecular mechanism of S. aureus Stp1 phosphatase and reveal the phosphorylated peptides for biochemistry study and inhibitor screening of Stp1.


    Organizational Affiliation

    University of the Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphorylated protein phosphataseA266Staphylococcus aureusMutation(s): 1 
Gene Names: 
prpCprpC_1BN1321_240063BTN44_06615CSC83_01010CSC87_08725EP54_08495EQ90_08165ERS072840_01404NCTC11940_01141NCTC13131_00423NCTC13196_02843NCTC9944_01222RK64_06500SAMEA1469870_01594SAMEA1531701_01402C7P97_09885DQV53_06510E3A28_02540E3K14_06010FA040_04580G0V24_07300G0X12_02540G0Z08_10970G0Z18_11445G6Y10_11525GF545_05680GF559_04870GO677_10370GO746_09405GO788_03515GO793_10355GO803_13910GO821_05845GO894_03380GO915_11975GO942_07250HMPREF2819_02510NCTC10654_01263NCTC10702_01924NCTC10988_01448SAMEA1029528_00202SAMEA1029547_01617SAMEA1029553_01716SAMEA1469884_02633SAMEA1531680_01545SAMEA1964876_01572SAMEA1965205_01586SAMEA1966505_01029SAMEA1969349_01558SAMEA1969845_01295SAMEA1971706_01764SAMEA1972827_01187SAMEA2076212_01583SAMEA2076218_01188SAMEA2076220_01573SAMEA2076226_00726SAMEA2076463_01324SAMEA2076464_01323SAMEA2076470_01543SAMEA2076472_01652SAMEA2076478_01635SAMEA2076480_01291SAMEA2076481_01945SAMEA2076743_01572SAMEA2076745_01900SAMEA2076746_01630SAMEA2076747_01335SAMEA2076749_01616SAMEA2076751_01427SAMEA2076752_01376SAMEA2076755_01227SAMEA2076756_01287SAMEA2076758_01127SAMEA2076759_01199SAMEA2076761_01551SAMEA2076762_01770SAMEA2076763_01702SAMEA2076764_01717SAMEA2076765_01766SAMEA2077023_01773SAMEA2077025_01497SAMEA2077027_01518SAMEA2077029_01493SAMEA2077031_01581SAMEA2077034_01733SAMEA2077035_01297SAMEA2077039_01433SAMEA2077040_01101SAMEA2077041_01747SAMEA2077044_01549SAMEA2077045_01594SAMEA2077046_01420SAMEA2077293_01622SAMEA2077294_01726SAMEA2077295_01424SAMEA2077297_01421SAMEA2077300_01725SAMEA2077301_01422SAMEA2077302_01607SAMEA2077303_01502SAMEA2077307_01453SAMEA2077832_01700SAMEA2078252_01746SAMEA2078256_01319SAMEA2078307_01631SAMEA2078308_01289SAMEA2078553_01222SAMEA2078558_01526SAMEA2078560_01555SAMEA2078569_01757SAMEA2078570_01658SAMEA2078572_01846SAMEA2078824_01321SAMEA2078837_01582SAMEA2079048_01539SAMEA2079051_01642SAMEA2079277_01357SAMEA2079291_01823SAMEA2079503_01657SAMEA2079507_01779SAMEA2079512_01630SAMEA2079517_01307SAMEA2079724_01158SAMEA2079727_00947SAMEA2079728_01500SAMEA2079732_01190SAMEA2079742_01460SAMEA2079946_01159SAMEA2079949_01144SAMEA2079951_01352SAMEA2079952_01192SAMEA2079957_01275SAMEA2079958_01000SAMEA2079960_01189SAMEA2079961_00534SAMEA2079968_01323SAMEA2080329_01242SAMEA2080330_01312SAMEA2080334_01539SAMEA2080433_01086SAMEA2080812_01260SAMEA2080898_02027SAMEA2080900_01580SAMEA2080904_01409SAMEA2080913_01469SAMEA2081043_01655SAMEA2081053_01562SAMEA2081054_01234SAMEA2081055_01519SAMEA2081060_00839SAMEA2081211_01561SAMEA2081213_01202SAMEA2081218_01063SAMEA2081341_01162SAMEA2081342_00955SAMEA2081349_01040SAMEA2081359_01206SAMEA2081362_01606SAMEA2081468_01317SAMEA2081474_01522SAMEA2081475_01598SAMEA2081476_00878SAMEA2081479_01390SAMEA2081480_01700SAMEA2081560_01303SAMEA2081561_01496SAMEA2081564_01716SAMEA2081567_01705SAMEA2081568_01713SAMEA2081569_01233SAMEA2081570_01716SAMEA2081571_01641SAMEA2081572_01453SAMEA2081573_01261SAMEA2081575_01580SAMEA2081577_01589SAMEA2081578_01302SAMEA2081579_01480SAMEA2081581_01386SAMEA2081582_01722SAMEA2081673_01040SAMEA2081674_01038SAMEA958766_00788SAMEA958770_01348SAMEA958772_01188SAMEA958778_00174SAMEA958779_01267SAMEA958785_00809SAMEA958793_01014SAMEA958798_01040SAMEA958804_00817SAMEA958810_01398SAMEA958836_00263SAMEA958838_00827SAMEA958845_00939SAMEA958846_01727SAMEA958848_01751SAMEA958855_00671SAMEA958858_00408SAMEA958870_02215SAMEA958898_00752SAMEA958906_01165SAMEA958924_01260SAMEA958925_01281SAMEA958951_01080SAMEA958953_01066SAMEA958961_01332SAMEA958979_00765SAMEA958987_01433SAMEA958995_00755SAST44_01247SAST45_01285

EC: 3.1.3.16
UniProt
Find proteins for Q9RL81 (Staphylococcus aureus)
Explore Q9RL81 
Go to UniProtKB:  Q9RL81
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.998α = 90
b = 37.745β = 102.87
c = 65.575γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-02 
  • Released Date: 2019-08-07 
  • Deposition Author(s): Yang, C.-G., yang, T.

Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references