4TVB

Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD, Putrescine and sym-Homospermidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.689 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism.

Krossa, S.Faust, A.Ober, D.Scheidig, A.J.

(2016) Sci Rep 6: 19501-19501

  • DOI: 10.1038/srep19501
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a pr ...

    The highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS). The structure of the bacterial enzyme does not possess a lysine residue in the active center and thus does not form an enzyme-substrate Schiff base intermediate as observed for the DHS. In contrast to the DHS the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial HSS. Crystal structures of Blastochloris viridis HSS (BvHSS) reveal two distinct substrate binding sites, one of which is highly specific for putrescine. BvHSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. The proposed reaction steps for the catalysis of BvHSS emphasize cation-π interaction through a conserved Trp residue as a key stabilizer of high energetic transition states.


    Organizational Affiliation

    Structural Biology-Zoological Institute, Kiel University, Am Botanischen Garten 11, 24118 Kiel, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homospermidine synthase
A, B
479Blastochloris viridisMutation(s): 0 
Gene Names: hss
EC: 2.5.1.44
Find proteins for O32323 (Blastochloris viridis)
Go to UniProtKB:  O32323
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

Download SDF File 
Download CCD File 
A
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PUT
Query on PUT

Download SDF File 
Download CCD File 
B
1,4-DIAMINOBUTANE
PUTRESCINE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
37Z
Query on 37Z

Download SDF File 
Download CCD File 
A
sym-homospermidine
C8 H21 N3
UODZHRGDSPLRMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.689 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.510α = 90.00
b = 109.254β = 90.00
c = 157.212γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-06-26 
  • Released Date: 2015-07-08 
  • Deposition Author(s): Krossa, S.

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection