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Putative DNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Putative DNA-binding domain [ 46954]
Superfamily:   Putative DNA-binding domain [ 46955] (7)
Families:   Domains B1 and B5 of PheRS-beta, PheT [ 46956]
  DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [ 46959]
  Dachshund-homology domain [ 74693] (2)
  DNA-binding N-terminal domain of transcription activators [ 46962] (4)
  Terminase gpNU1 subunit domain [ 74696]
  Excisionase-like [ 46891] (2)
  N-terminal subdomain of bacterial translation initiation factor IF2 [ 89006]


Superfamily statistics
Genomes (3,234) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 23,551 208,282 22
Proteins 22,702 202,870 20


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Phenylalanine--tRNA ligase0InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormal muscle tone0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.07374Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.02362Moderately InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0008547InformativeDirect
Mammalian Phenotype (MP)abnormal physiological response to xenobiotic0.01574InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult segment0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-oxygen bonds0InformativeDirect
Enzyme Commission (EC)Phenylalanine--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009061 SSF46955 Protein matches
Abstract

A putative DNA-binding domain with a conserved structure is found in several different protein families. The core structure of the domain consists of a three-helical fold that is architecturally similar to that of the "winged-helix" fold, but is topologically distinct. Representatives of this domain can be found in domains B1 and B5 from the beta subunit of phenylalanine-tRNA synthetases [PubMed11679717], the C-terminal region of the DNA/RPA-binding domain of the DNA excision repair factor XPA [PubMed10563794], the N-terminal domain of the transcriptional activators BmrR and MtaN [PubMed11201751], the most conserved domain of the retinal development protein Dachshund [PubMed12057194], and the DNA-binding domain of the gpNU1 subunit from the bacteriophage lambda viral packing protein terminase [PubMed12049735].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 20 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Putative DNA-binding domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 20 hidden Markov models representing the Putative DNA-binding domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]