PDBsum entry 4xrg

Transferase

PDB id: 4xrg

Contents

Protein chains

474 a.a.

Ligands

NAD ×2

AG2-PUT ×2

1PS ×2

ACT ×2

Waters ×1150

PDB id:

4xrg

Name:

Transferase

Title:

Crystal structure of the homospermidine synthase (hss) variant h296s from blastochloris viridis in complex with NAD, putrescine and agmatine

Structure:

Homospermidine synthase. Chain: a, b. Synonym: hss. Engineered: yes. Mutation: yes

Source:

Blastochloris viridis. Organism_taxid: 1079. Gene: hss. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.30Å R-factor: 0.162 R-free: 0.198

Authors:

S.Krossa

Key ref:

S.Krossa et al. (2016). Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism. Sci Rep, 6, 19501. PubMed id: 26776105 DOI: 10.1038/srep19501

Date:

21-Jan-15 Release date: 27-Jan-16

Protein chains

O32323  (HSS_BLAVI) -  Homospermidine synthase from Blastochloris viridis

Seq: 477 a.a.

Struc: 474 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.44 - homospermidine synthase.
• Pathway: EC 2.5.1.44 and EC 2.5.1.45
• Reaction:
  1. 2 putrescine = sym-homospermidine + NH4⁺
  2. putrescine + spermidine = sym-homospermidine + propane-1,3-diamine

2 × putrescine (Bound ligand (Het Group name = AG2) matches with 66.67% similarity) = sym-homospermidine + NH4(+) (Bound ligand (Het Group name = 1PS) matches with 50.00% similarity)

putrescine (Bound ligand (Het Group name = AG2) matches with 66.67% similarity) + spermidine (Bound ligand (Het Group name = 1PS) matches with 53.33% similarity) = sym-homospermidine + propane-1,3-diamine

• Cofactor: NAD(+)

NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/srep19501

Sci Rep 6:19501 (2016)

PubMed id: 26776105

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

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

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 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.