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36  structures 2472  species 2  interactions 9715  sequences 73  architectures

Clan: DinB (CL0310)

Summary

DinB-like superfamily Add an annotation

This superfamily are thought to be metalloenzymes. They possess a four helical bundle core structure with a beta hairpin. Members of the superfamily have a predicted active site composed of three histidines that chelate Nickel or Zinc. In some cases these histidines are replaced with Aspartate or Glutamate. Mostly they form a dimeric structure. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of the clan. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). Most (but not all) clan members seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The proteins that share the fold exhibit four different quaternary structures: monomeric and three different dimeric forms [1].

This clan contains 8 families and the total number of domains in the clan is 9715. The clan was built by A Bateman.

Literature references

  1. Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS;, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:219-224.: The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. PUBMED:20208147 EPMC:20208147

Members

This clan contains the following 8 member families:

DinB DinB_2 DUF1569 DUF1572 DUF1706 DUF1993 DUF664 MDMPI_N

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
DinB_2 (PF12867) 3722 (38.3%) View
MDMPI_N (PF11716) 2030 (20.9%) View
DinB (PF05163) 1291 (13.3%) View
DUF664 (PF04978) 958 (9.9%) View
DUF1706 (PF08020) 927 (9.5%) View
DUF1993 (PF09351) 472 (4.9%) View
DUF1572 (PF07609) 202 (2.1%) View
DUF1569 (PF07606) 113 (1.2%) View
Total: 8 Total: 9715 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 2 interactions for this clan. More...

Interacting families
A B
DUF1993 DUF1993
DinB DinB

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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