PDBsum entry 3omw

Go to PDB code: 
protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
190 a.a. *
Waters ×15
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of ssu72, an essential eukaryotic phosphat specific for thE C-terminal domain of RNA polymerase ii
Structure: Cg14216. Chain: a, b, c, d. Synonym: ld40846p. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: cg14216, dmel_cg14216. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.87Å     R-factor:   0.225     R-free:   0.286
Authors: Y.Zhang,M.Zhang,Y.Zhang
Key ref: Y.Zhang et al. (2011). Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue. Biochem J, 434, 435-444. PubMed id: 21204787
27-Aug-10     Release date:   19-Jan-11    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9VWE4  (Q9VWE4_DROME) -  LD40846p
195 a.a.
190 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.  - Protein-serine/threonine phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [a protein]-serine/threonine phosphate + H2O = [a protein]- serine/threonine + phosphate
[a protein]-serine/threonine phosphate
+ H(2)O
= [a protein]- serine/threonine
+ phosphate
   Enzyme class 3: E.C.  - 4-nitrophenylphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-nitrophenyl phosphate + H2O = 4-nitrophenol + phosphate
4-nitrophenyl phosphate
+ H(2)O
= 4-nitrophenol
+ phosphate
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     dephosphorylation of RNA polymerase II C-terminal domain   2 terms 
  Biochemical function     hydrolase activity     4 terms  


Biochem J 434:435-444 (2011)
PubMed id: 21204787  
Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue.
Y.Zhang, M.Zhang, Y.Zhang.
Reversible phosphorylation of the CTD (C-terminal domain) of the eukaryotic RNA polymerase II largest subunit represents a critical regulatory mechanism during the transcription cycle and mRNA processing. Ssu72 is an essential phosphatase conserved in eukaryotes that dephosphorylates phosphorylated Ser5 of the CTD heptapeptide. Its function is implicated in transcription initiation, elongation and termination, as well as RNA processing. In the present paper we report the high resolution X-ray crystal structures of Drosophila melanogaster Ssu72 phosphatase in the apo form and in complex with an inhibitor mimicking the transition state of phosphoryl transfer. Ssu72 facilitates dephosphorylation of the substrate through a phosphoryl-enzyme intermediate, as visualized in the complex structure of Ssu72 with the oxo-anion compound inhibitor vanadate at a 2.35 Å (1 Å=0.1 nm) resolution. The structure resembles the transition state of the phosphoryl transfer with vanadate exhibiting a trigonal bi-pyramidal geometry covalently bonded to the nucleophilic cysteine residue. Interestingly, the incorporation of oxo-anion compounds greatly stabilizes a flexible loop containing the general acid, as detected by an increase of melting temperature of Ssu72 detected by differential scanning fluorimetry. The Ssu72 structure exhibits a core fold with a similar topology to that of LMWPTPs [low-molecular-mass PTPs (protein tyrosine phosphatases)], but with an insertion of a unique 'cap' domain to shelter the active site from the solvent with a deep groove in between where the CTD substrates bind. Mutagenesis studies in this groove established the functional roles of five residues (Met17, Pro46, Asp51, Tyr77 and Met85) that are essential specifically for substrate recognition.