PDBsum entry 6t1b

Hydrolase

PDB id: 6t1b

Contents

Protein chain

271 a.a.

Ligands

NOS

Metals

_ZN ×2

Waters ×208

PDB id:

6t1b

Name:

Hydrolase

Title:

Crystal structure of ylmd from geobacillus stearothermophilus in complex with inosine

Structure:

Ylmd. Chain: a. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.20Å R-factor: 0.154 R-free: 0.167

Authors:

S.Reikine,Y.Modis

Date:

03-Oct-19 Release date: 29-Jan-20

Protein chain

P84138  (PURNU_GEOS3) -  Purine nucleoside phosphorylase YlmD from Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10)

Seq: 274 a.a.

Struc: 271 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate
• Enzyme class 2: E.C.2.4.2.28 - S-methyl-5'-thioadenosine phosphorylase.
• Reaction: S-methyl-5'-thioadenosine + phosphate = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + adenine

S-methyl-5'-thioadenosine + phosphate (Bound ligand (Het Group name = NOS) matches with 77.27% similarity) = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + adenine

• Enzyme class 3: E.C.3.5.4.4 - adenosine deaminase.
• Reaction:
  1. adenosine + H2O + H⁺ = inosine + NH4⁺
  2. 2'-deoxyadenosine + H2O + H⁺ = 2'-deoxyinosine + NH4⁺

adenosine + H2O + H(+) = inosine (Bound ligand (Het Group name = NOS) corresponds exactly) + NH4(+)

2'-deoxyadenosine (Bound ligand (Het Group name = NOS) matches with 85.00% similarity) + H2O + H(+) = 2'-deoxyinosine + NH4(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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