4XQE

Crystal Structure of the Homospermidine Synthase (HSS) variant H296S from Blastochloris viridis in Complex with NAD and Agmatine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    4PLP, 4TVB, 4XQ9, 4XQC, 4XQE, 4XQG, 4XR4, 4XRG

  • 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 prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homospermidine synthaseA, B474Blastochloris viridisMutation(s): 1 
Gene Names: hss
EC: 2.5.1.44
UniProt
Find proteins for O32323 (Blastochloris viridis)
Explore O32323 
Go to UniProtKB:  O32323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
1PS
Query on 1PS

Download Ideal Coordinates CCD File 
F [auth A],
I [auth A],
P [auth B]
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
AG2
Query on AG2

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth B],
O [auth B]
AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.251α = 90
b = 110.102β = 90
c = 157.851γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-01-27 
  • Deposition Author(s): Krossa, S.

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection