PDBsum entry 7f3v

Hydrolase

PDB id: 7f3v

Contents

Protein chains

242 a.a.

Ligands

EPZ ×4

PO4 ×2

TRS ×2

Waters ×838

PDB id:

7f3v

Name:

Hydrolase

Title:

Crystal structure of yfih with c107a mutation in complex with endogenous udp-murnac

Structure:

Purine nucleoside phosphorylase yfih. Chain: a, b, c, d. Synonym: adenosine deaminase yfih,polyphenol oxidase yfih,s-methyl- 5'-thioadenosine phosphorylase yfih. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.47Å R-factor: 0.187 R-free: 0.214

Authors:

M.S.Lee,K.Y.Hsieh,C.I.Chang

Key ref:

M.S.Lee et al. Structural basis for the peptidoglycan editing activi yfih. Biorxiv, . PubMed id: 35164571

Date:

17-Jun-21 Release date: 29-Dec-21

Protein chains

P33644  (POLOX_ECOLI) -  Purine nucleoside phosphorylase YfiH from Escherichia coli (strain K12)

Seq: 243 a.a.

Struc: 242 a.a.*

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

Enzyme reactions

• Enzyme class 2: 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

purine D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + alpha- D-ribose 1-phosphate

purine 2'-deoxy-D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

• Enzyme class 3: 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 (Bound ligand (Het Group name = PO4) corresponds exactly) + phosphate = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + adenine

• Enzyme class 4: E.C.3.5.4.4 - adenosine deaminase.
• Reaction:
  1. adenosine + H2O + H⁺ = inosine + NH4⁺
  2. 2'-deoxyadenosine + 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