2CMH

Crystal Structure of Spermidine Synthase from Helicobacter Pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Helicobacter Pylori Spermidine Synthase: A Rossmann-Like Fold with a Distinct Active Site

Lu, P.-K.Tsai, J.-Y.Chien, H.Y.Huang, H.Chu, C.-H.Sun, Y.-J.

(2007) Proteins: Struct., Funct., Bioinf. 67: 743

  • DOI: 10.1002/prot.21315
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the transfer of the aminopropyl group from decarboxylated S-adenosylmethionine to putrescine during spermidine biosynthesis. Helicobacter pylori PAPT (HpPAPT) has a low sequence ...

    Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the transfer of the aminopropyl group from decarboxylated S-adenosylmethionine to putrescine during spermidine biosynthesis. Helicobacter pylori PAPT (HpPAPT) has a low sequence identity with other PAPTs and lacks the signature sequence found in other PAPTs. The crystal structure of HpPAPT, determined by multiwavelength anomalous dispersion, revealed an N-terminal beta-stranded domain and a C-terminal Rossmann-like domain. Structural comparison with other PAPTs showed that HpPAPT has a unique binding pocket between two domains, numerous non-conserved residues, a less acidic electrostatic surface potential, and a large buried space within the structure. HpPAPT lacks the gatekeeping loop that facilitates substrate binding in other PAPTs. PAPTs are essential for bacterial cell viability; thus, HpPAPT may be a potential antimicrobial drug target for H. pylori owing to its characteristic PAPT sequence and distinct conformation.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPERMIDINE SYNTHASE
A, B, C
262Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: speE
Find proteins for O25503 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25503
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.526α = 90.00
b = 126.468β = 90.00
c = 143.948γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-05-08 
  • Released Date: 2007-05-08 
  • Deposition Author(s): Sun, Y.-J., Lu, P.-K.

Revision History 

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance