Brand  (β version)

PDB ID: 4GIM

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Ligands
Code Name Style Show Link
MN Manganese (II) ion PoSSuM
PSU Pseudouridine-5'-monophosphate PoSSuM
Non-standard Residues
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Glycosylation
Code Name Emphasize
Modification
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Structure summary

Code : 4GIM   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate
Release Data : 2012-10-31
Compound :
mol_id molecule chains synonym
1 Pseudouridine-5'-phosphate glycosidase A,B,C pseudouridine monophosphate glycosidase, PsiMP glycosidase
ec: 3.2.-.-
mutation: K166A
Source :
mol_id organism_scientific expression_system
1 Escherichia coli  (taxid:562) Escherichia coli  (taxid:469008)
gene: b2165, JW2152, psuG, yeiN
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: THT
Authors : Huang, S., Mahanta, N., Begley, T.P., Ealick, S.E.
Keywords : alpha-beta-alpha sandwich fold, HYDROLASE
Exp. method : X-RAY DIFFRACTION ( 1.802 Å )
Citation :

Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.

Huang, S.,Mahanta, N.,Begley, T.P.  et al.
(2012)  Biochemistry  51 : 9245 - 9255

PubMed: 23066817
DOI: 10.1021/bi3006829

Reaction

Chain : A, B, C
UniProt : P33025 (PSUG_ECOLI)
Reaction: EC: Evidence:
Physiological Direction:
D-ribose 5-phosphate + uracil = psi-UMP + H2O 4.2.1.70 HAMAP-Rule:MF_01876, PubMed:18591240, PubMed:23066817
-
Cofactor: Evidence: Note:
Co(2+) ECO:0000255 | HAMAP-Rule:MF_01876
ECO:0000269 | PubMed:18591240
ECO:0000269 | PubMed:23066817
ECO:0000269 | PubMed:18591240
ECO:0000269 | PubMed:23066817
ECO:0000269 | PubMed:18591240
ECO:0000269 | PubMed:23066817
Binds 1 manganese ion per subunit. Can also use Fe(2+) and Co(2+). The unusual metal binding site is heavily hydrated, coordinated with an aspartate side chain and five water molecules, and likely plays a role in anchoring the PsiMP phosphate.