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PDBsum entry 2lto

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protein links
Transcription/transferase PDB id
2lto
Jmol
Contents
Protein chains
58 a.a.
13 a.a.
PDB id:
2lto
Name: Transcription/transferase
Title: Tdrd3 complex
Structure: Tudor domain-containing protein 3. Chain: a. Fragment: tudor domain residues 554-608. Engineered: yes. DNA-directed RNA polymerase ii subunit rpb1. Chain: b. Fragment: unp residues 1804-1816. Synonym: RNA polymerase ii subunit b1, DNA-directed RNA pol subunit a, DNA-directed RNA polymerase iii largest subunit,
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: tdrd3. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606
NMR struc: 20 models
Authors: T.Sikorsky
Key ref: T.Sikorsky et al. (2012). Recognition of asymmetrically dimethylated arginine by TDRD3. Nucleic Acids Res, 40, 11748-11755. PubMed id: 23066109
Date:
30-May-12     Release date:   16-Jan-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9H7E2  (TDRD3_HUMAN) -  Tudor domain-containing protein 3
Seq:
Struc:
 
Seq:
Struc:
651 a.a.
58 a.a.*
Protein chain
Pfam   ArchSchema ?
P24928  (RPB1_HUMAN) -  DNA-directed RNA polymerase II subunit RPB1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1970 a.a.
13 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chain B: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 2: Chain B: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
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

 

 
    reference    
 
 
Nucleic Acids Res 40:11748-11755 (2012)
PubMed id: 23066109  
 
 
Recognition of asymmetrically dimethylated arginine by TDRD3.
T.Sikorsky, F.Hobor, E.Krizanova, J.Pasulka, K.Kubicek, R.Stefl.
 
  ABSTRACT  
 
Asymmetric dimethylarginine (aDMA) marks are placed on histones and the C-terminal domain (CTD) of RNA Polymerase II (RNAP II) and serve as a signal for recruitment of appropriate transcription and processing factors in coordination with transcription cycle. In contrast to other Tudor domain-containing proteins, Tudor domain-containing protein 3 (TDRD3) associates selectively with the aDMA marks but not with other methylarginine motifs. Here, we report the solution structure of the Tudor domain of TDRD3 bound to the asymmetrically dimethylated CTD. The structure and mutational analysis provide a molecular basis for how TDRD3 recognizes the aDMA mark. The unique aromatic cavity of the TDRD3 Tudor domain with a tyrosine in position 566 creates a selectivity filter for the aDMA residue. Our work contributes to the understanding of substrate selectivity rules of the Tudor aromatic cavity, which is an important structural motif for reading of methylation marks.