SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from Please contact us if you experience any problems.

NAC domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   NAC domain [ 101940]
Superfamily:   NAC domain [ 101941]
Families:   NAC domain [ 101942]

Superfamily statistics
Genomes (59) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 8,243 14,877 1
Proteins 8,116 14,676 1

Functional annotation
General category Information
Detailed category Translation

Function annotation of SCOP domain superfamilies

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot axis0.5349Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.9511Least InformativeInherited
Plant ANatomical entity (PAN)root system1Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure1Least InformativeInherited
Plant ANatomical entity (PAN)portion of vascular tissue0.00000003168InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.0000002663InformativeDirect
Plant ANatomical entity (PAN)root tip0.0000004618InformativeDirect
Plant ANatomical entity (PAN)root stele0.0000006354Highly InformativeDirect
Plant ANatomical entity (PAN)shoot axis stele0.0000008702Highly InformativeDirect
Plant ANatomical entity (PAN)primary root0.0002695Highly InformativeDirect
Plant ANatomical entity (PAN)plant axis elongation zone0.0002937Highly InformativeDirect

Document: AP annotation of SCOP domains

InterPro annotation
Cross references IPR003441 SSF101941 Protein matches

The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) [PubMed9212461]. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [PubMed11114891,PubMed12175016].

The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D [PubMed10660065]. The DBD is contained within a 60 amino acid region located within subdomains D and E [PubMed12175016]. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [PubMed15083810].

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 · Arabidopsis Plant Ontology (AP) ]

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 2 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 NAC 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 2 hidden Markov models representing the NAC 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 · Arabidopsis Plant Ontology (AP) · Internal database links ]