PDBsum entry: 2ght

Hydrolase

PDB id: 2ght

Contents

Protein chains

180 a.a. *

Ligands

SER-PRO-THR-SEP-PRO

SER-TYR-SER-PRO-THR-SEP-PRO-SER

Metals

_MG ×2

Waters ×245

* Residue conservation analysis

PDB id:

2ght

Name:

Hydrolase

Title:

Ctd-specific phosphatase scp1 in complex with peptide from c-terminal domain of RNA polymerase ii

Structure:

Carboxy-terminal domain RNA polymerase ii polypeptide a small phosphatase 1. Chain: a, b. Synonym: nuclear lim interactor-interacting factor 3, nli- interacting factor 3, nli-if. Engineered: yes. Mutation: yes. DNA-directed RNA polymerase ii largest subunit. Chain: c, d.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ctdsp1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.216 R-free: 0.232

Authors:

Y.Zhang,J.P.Noel

Key ref:

Y.Zhang et al. (2006). Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Mol Cell, 24, 759-770. PubMed id: 17157258 DOI: 10.1016/j.molcel.2006.10.027

Date:

27-Mar-06 Release date: 05-Dec-06

Protein chains

Q9GZU7  (CTDS1_HUMAN) -  Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1

Seq: 261 a.a.

Struc: 180 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.3.16 - Phosphoprotein phosphatase.
• Reaction: A phosphoprotein + H₂O = a protein + phosphate

phosphoprotein + H(2)O = protein + phosphate (Bound ligand (Het Group name = SEP) matches with 50.00% similarity)

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: phosphatase activity (1 term)

Added reference

DOI no: 10.1016/j.molcel.2006.10.027

Mol Cell 24:759-770 (2006)

PubMed id: 17157258

Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1.

Y.Zhang, Y.Kim, N.Genoud, J.Gao, J.W.Kelly, S.L.Pfaff, G.N.Gill, J.E.Dixon, J.P.Noel.

ABSTRACT

Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.

Selected figure(s)

Figure 2.
Figure 2. Structures of Human Scp1 Complexed to CTD Phosphopeptides
(A) Stereo ribbon diagram of human Scp1 bound to a CTD phosphopeptide with helices as red coils and β strands as blue arrows. The three-stranded insert is labeled βID1-3. The CTD peptide is a stick diagram with color-coded bonds. Yellow is carbon, red is oxygen, blue is nitrogen, and magenta is phosphorus. The Mg^2+ ion is shown as a magenta van der Waals sphere.
(B) Model of the monophosphorylated CTD peptide complex (P.Ser[5]) as a half-colored bond diagram with the blue SIGMAA weighted 2F[o] − F[c] electron-density map contoured at 1σ. An intramolecular hydrogen bond between the Ser[2] and Thr[4] is shown as red cylinders.
(C) Accessible surface of Scp1 bound to monophosphorylated P.Ser[5] CTD peptide. Surfaces conserved between human Fcp1 and human Scp1 are orange, and chemically similar residues are pink. Phe106 is yellow. The peptide is shown as half-colored bonds with carbon atoms light green.
(D) Model of the doubly phosphorylated 14-mer CTD peptide complex (P.Ser[5]-P.Ser[5]) as a half-colored bond diagram with the blue SIGMAA-weighted 2F[o] − F[c] electron-density map contoured at 1σ.

Figure 4.
Figure 4. Reaction and Binding Mechanisms of Scp1
(A) Reaction mechanism of Scp1. The active site geometry, water coordination, and position of Asp206 supports its participation as a general base for activating a water for breakdown of the mixed anhydride intermediate formed after nucleophilic attack of Asp96 on P.Ser[5]. Alternatively, the residue equivalent to Asp98 may function as the general base for this final catalytic step (Wang et al., 2002).
(B) Pro[3] binding pocket of Scp1 and comparison with Fcp1. The lavender ribbon underlies a transparent surface used to illustrate the steric volume surrounding the Pro[3] moiety. Peptide and side chains are shown as half-colored bonds with green highlighting carbon for the peptide and yellow highlighting carbon for Scp1. The equivalent residues in human Fcp1 are labeled blue in italic.
(C) Scp1 residues involved in the binding of the phospho-CTD. Intermolecular hydrogen bonds are shown as rendered green cylinders, and an intramolecular hydrogen bond in the CTD peptide is shown as rendered red cylinders.

The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 24, 759-770) copyright 2006.

Figures were selected by the author.