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325  structures 504  species 7  interactions 17304  sequences 682  architectures

Clan: Tudor (CL0049)

Summary

Tudor domain 'Royal family' Add an annotation

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

This clan contains 14 families and the total number of domains in the clan is 17304. The clan was built by RD Finn and A Bateman.

Literature references

  1. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP; , Trends Biochem Sci 2003;28:69-74.: The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. PUBMED:12575993 EPMC:12575993
  2. Eissenberg JC; , Gene 2001;275:19-29.: Molecular biology of the chromo domain: an ancient chromatin module comes of age. PUBMED:11574148 EPMC:11574148

Members

This clan contains the following 14 member families:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_shadow DUF1325 DUF4537 MBT PWWP Rad9_Rad53_bind RBB1NT SMN TUDOR Tudor-knot

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
Chromo (PF00385) 5794 (33.5%) View
TUDOR (PF00567) 3295 (19.0%) View
PWWP (PF00855) 2569 (14.8%) View
MBT (PF02820) 2104 (12.2%) View
Tudor-knot (PF11717) 1173 (6.8%) View
Agenet (PF05641) 609 (3.5%) View
Chromo_shadow (PF01393) 489 (2.8%) View
SMN (PF06003) 460 (2.7%) View
DUF1325 (PF07039) 328 (1.9%) View
RBB1NT (PF08169) 171 (1.0%) View
DUF4537 (PF15057) 111 (0.6%) View
53-BP1_Tudor (PF09038) 89 (0.5%) View
Rad9_Rad53_bind (PF08605) 79 (0.5%) View
7kD_DNA_binding (PF02294) 33 (0.2%) View
Total: 14 Total: 17304 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 7 interactions for this clan. More...

Interacting families
A B
Chromo_shadow Chromo_shadow
ENT
CAF-1_p150
MBT MBT
TUDOR SNase
TUDOR
Chromo Chromo

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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