4NFW

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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This is version 1.1 of the entry. See complete history. 


Literature

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Hong, M.K., Ribeiro, A.J.M., Kim, J.K., Ngo, H.P.T., Kim, J., Lee, C.H., Ahn, Y.J., Fernandes, P.A., Li, Q., Ramos, M.J., Kang, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1297-1310

  • DOI: 10.1107/S1399004714002570
  • Primary Citation of Related Structures:  
    4NFW, 4NFX

  • PubMed Abstract: 

    • YmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner ...

    YmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner. The structures of YmfB alone and in complex with three sulfates and two manganese ions determined by X-ray crystallography, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB. Mass-spectrometric analysis confirmed that water attacks the terminal phosphates of GTP and GDP sequentially. Kinetic analysis of binding-site mutants showed that no individual residue is absolutely required for catalytic activity, suggesting that protein residues do not participate in the deprotonation of the attacking water. Thermodynamic integration calculations show that a hydroxyl ion bound to two divalent metal ions attacks the phosphate directly without the help of a nearby catalytic base.

    Organizational Affiliation: 

    Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative Nudix hydrolase ymfB
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
153Escherichia coli str. 'clone D i14Mutation(s): 0 
Gene Names: i14_1356
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth C] , BB [auth I] , CB [auth I] , DA [auth D] , EA [auth D] , FA [auth D] , FB [auth J] , GB [auth J] , 
AA [auth C],  BB [auth I],  CB [auth I],  DA [auth D],  EA [auth D],  FA [auth D],  FB [auth J],  GB [auth J],  HB [auth J],  IA [auth E],  JA [auth E],  KA [auth E],  KB [auth K],  LB [auth K],  MB [auth K],  NA [auth F],  O [auth A],  OA [auth F],  OB [auth L],  P [auth A],  PA [auth F],  PB [auth L],  Q [auth A],  QB [auth L],  SA [auth G],  T [auth B],  TA [auth G],  U [auth B],  UA [auth G],  V [auth B],  XA [auth H],  Y [auth C],  YA [auth H],  Z [auth C],  ZA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
AB [auth I] , BA [auth D] , CA [auth D] , DB [auth J] , EB [auth J] , GA [auth E] , HA [auth E] , IB [auth K] , 
AB [auth I],  BA [auth D],  CA [auth D],  DB [auth J],  EB [auth J],  GA [auth E],  HA [auth E],  IB [auth K],  JB [auth K],  LA [auth F],  M [auth A],  MA [auth F],  N [auth A],  NB [auth L],  QA [auth G],  R [auth B],  RA [auth G],  S [auth B],  VA [auth H],  W [auth C],  WA [auth H],  X [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.387α = 90
b = 111.387β = 90
c = 247.489γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references