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Self-stabilizing region of a protein that binds to specific DNA sequences
A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded
DNA-binding_domain
Protein that regulates the rate of DNA transcription
sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to DNA sequences
Transcription_factor
Proteins that bind with DNA
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific
DNA-binding_protein
Region of a protein which can bind to biomolecules with chemical specificity
molecular biology, binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. A protein domain is a part of a
Binding_domain
Small structural protein motif found mostly in transcriptional proteins
individual zinc finger domains typically occur as tandem repeats with two, three, or more fingers comprising the DNA-binding domain of the protein. These
Zinc_finger
Restriction enzyme
N-terminal DNA-binding domain and a non sequence-specific DNA cleavage domain at the C-terminal. Once the protein is bound to duplex DNA via its DNA-binding domain
FokI
which must comprise a DNA-binding domain to give sequence specificity and a nuclease domain for DNA cleavage. DNA-binding domains including the basic helix-loop-helix
Chimeric_nuclease
Protein domain
Domain (bZIP domain) is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding
BZIP_domain
One of many possible double helical structures of DNA
Z-RNA and the B–Z junction. Biological studies suggested that the Z-DNA binding domain of ADAR1 may localize this enzyme that modifies the sequence of the
Z-DNA
a DNA-binding domain and a regulatory domain, also known as an effector domain or modulatory domain. The DNA-binding domain targets a specific DNA sequence
Artificial transcription factor
Artificial_transcription_factor
Protein-coding gene in humans
by the CXXC1 gene. Proteins that contain a CXXC motif within their DNA-binding domain, such as CXXC1, recognize CpG sequences and regulate gene expression
CXXC1
InterPro Family
SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member
Squamosa promoter binding protein
Squamosa_promoter_binding_protein
Protein family
various binding modes in vivo. SSB protein domains in bacteria are important in its function of maintaining DNA metabolism, more specifically DNA replication
Single-strand DNA-binding protein
Single-strand_DNA-binding_protein
Protein-coding gene in humans
protein contains three domains, an N-terminal DNA-binding domain, a central transcriptional activation domain and a C-terminal domain involved in transcriptional
MYB_(gene)
Protein that increases transcription of a gene or set of genes
"activating region" or "activation domain". Most activators function by binding sequence-specifically to a regulatory DNA site located near a promoter and
Activator_(genetics)
DNA-binding protein
repressor (LacI) operates by a helix-turn-helix motif in its DNA-binding domain, binding base-specifically to the major groove of the operator region
Lac_repressor
Artificial enzymes
fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger-domains can be engineered to target specific desired DNA sequences and this
Zinc-finger_nuclease
Protein-coding gene in the species Homo sapiens
RFX family member 8, lacking RFX DNA binding domain is a protein that in humans is encoded by the RFX8 gene. GRCh38: Ensembl release 89: ENSG00000196460
RFX family member 8, lacking RFX DNA binding domain
RFX_family_member_8,_lacking_RFX_DNA_binding_domain
a DNA binding domain that targets specific sequences and an effector domain that modifies epigenomic features. Currently, three major groups of DNA binding
Epigenome_editing
Protein family
precise function of the protein domain SAND remains to be determined. Nevertheless, it is thought to be a DNA binding domain despite its beta structure. This
SAND DNA-binding protein domain
SAND_DNA-binding_protein_domain
Restriction enzyme
has two domains, N-terminal and C-terminal, linked through a hinge loop. The N-terminal effector-binding domain has an archetypal DNA-binding pseudobarrel
R.EcoRII
Protein domain
domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA-editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of
Adenosine deaminase z-alpha domain
Adenosine_deaminase_z-alpha_domain
Structural motif capable of binding DNA
a DNA-binding domain (DBD). Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The
Helix-turn-helix
Family of proteins
factors which have a similarly structured DNA-binding domain, despite having a very different mechanism of DNA-binding. These related transcription factors
Winged-helix transcription factors
Winged-helix_transcription_factors
Protein family
factors that have well-conserved homeodomains. The Pou domain is a bipartite DNA binding domain found in these proteins. The acronym POU is derived from
POU_domain
Chromatin remodeling protein that is widely conserved across many eukaryotic organisms
named for three of its protein domains: two tandem chromodomains, its ATPase catalytic domain, and its DNA-binding domain (Figure 1). The CHD1 remodeler
CHD1
Prokaryotic protein
DNA-binding domain and a dimerization domain. The dimerization domain binds to other LexA polypeptides to form dumbbell shaped dimers. The DNA-binding domain is
LexA_repressor
The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein family. This group of proteins
Ribose_repressor
Protein
receptors. (C) DNA-binding domain (DBD): Highly conserved domain containing two zinc fingers that binds to specific sequences of DNA called hormone response
Nuclear_receptor
Protein domain
is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a
3H_domain
DNA binding domain
The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors (≥40 species) (Pfam PF02362) combined with other
B3_domain
Protein family
In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. It is present in transcription
LuxR-type DNA-binding HTH domain
LuxR-type_DNA-binding_HTH_domain
Class of proteins
"Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray
Single-stranded binding protein
Single-stranded_binding_protein
Molecular biology technique
called the DNA-binding domain (DBD or often also abbreviated as BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS
Two-hybrid_screening
Gene of insects
of these are transcription factors with a zinc finger DNA-binding domain (known as the DM domain) and are involved in sex-specific differentiation. Verhulst
Doublesex
Protein domain
NH2-terminal of D-domain. This domain in the thyroid hormone receptor (TR) connects the DNA-binding domain (DBD) with the ligand-binding domain (LBD). It can
D_domain
Family of proteins
domains of interest: a DNA-binding domain, a caspase-cleaved domain (see below), an auto-modification domain, and a catalytic domain. The DNA-binding
Poly_(ADP-ribose)_polymerase
Method for identifying the sequence-specific target site of a DNA-binding domain
is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as
Bacterial_one-hybrid_system
Protein family
The Methyl-CpG-binding domain (MBD) in molecular biology binds to DNA that contains one or more symmetrically methylated CpGs. MBD has negligible non-specific
Methyl-CpG-binding_domain
Protein domain which is involved in DNA binding
protein domain which is involved in DNA binding. The domain is composed of approximately 75 amino acid residues that collectively mediate the DNA-binding of
HMG-box
Regions of DNA capable of binding to biomolecules
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that
DNA_binding_site
Protein domain
the DNA binding affinity of the N-terminal domain. FadR is a member of the GntR family of bacterial transcription regulators. The DNA-binding domain is
Fatty acid metabolism regulator protein FadR
Fatty_acid_metabolism_regulator_protein_FadR
Protein-coding gene in the species Homo sapiens
Methyl-CpG-binding domain protein 2 is a protein that in humans is encoded by the MBD2 gene. DNA methylation is the major modification of eukaryotic genomes
Methyl-CpG-binding domain protein 2
Methyl-CpG-binding_domain_protein_2
causes a conformational change that affects the DNA-binding domain so that TetR is no longer able to bind DNA. As a result, TetA and TetR are expressed. There
TetR
Synthetic DNA transposon for vertebrate genetic modification
the DNA-binding motifs for recognition of the direct repeats (DRs), was restored in steps 5->8. The last two steps restored the catalytic domain, which
Sleeping Beauty transposon system
Sleeping_Beauty_transposon_system
glucose concentrations. Upon arabinose binding to AraC, the N-terminal arm of AraC is released from its DNA binding domain via a “light switch” mechanism. This
PBAD_promoter
factors to inhibit DNA binding of bHLH proteins. ID proteins also contain the HLH-dimerization domain but lack the basic DNA-binding domain and thus regulate
Inhibitor of DNA-binding protein
Inhibitor_of_DNA-binding_protein
Proteins that bind DNA
factors are defined by the presence of a DNA-binding domain; in this case, it is the WRKY domain. The WRKY domain was named in 1996 after the almost invariant
WRKY_transcription_factor
Bacterial DNA primase
C-terminal domain (residues 434–581) is responsible for the noncovalent binding of DnaG to the DnaB helicase protein. The zinc-binding domain, the domain responsible
DnaG
Class of enzymes
catalytic core domain (RNaseH fold), a C-terminal DNA-binding domain (SH3 fold). Crystal and NMR structures of the individual domains and 2-domain constructs
Integrase
DNA sequence (or subset thereof), to which the domain is specific
A recognition sequence is a DNA sequence to which a structural motif of a DNA-binding domain exhibits binding specificity. Recognition sequences are palindromes
Recognition_sequence
Enzymes that cleave DNA in specific ways
specific sequences of DNA. They are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain (a nuclease which cuts DNA strands). Transcription
Transcription activator-like effector nuclease
Transcription_activator-like_effector_nuclease
Protein found in humans
Transactive response DNA binding protein 43 kDa (TAR DNA-binding protein 43 or TDP-43) is a protein that in humans is encoded by the TARDBP gene. TDP-43
TAR_DNA-binding_protein_43
Protein domain
The 7 kDa DNA-binding proteins are a family of DNA-binding proteins from Sulfolobales archaea. These proteins bind DNA in a mostly sequence-independent
7_kDa_DNA-binding_protein
Protein family
In molecular biology, the KilA-N domain is a conserved DNA-binding domain found at the N-terminus of the poxvirus D6R/NIR proteins. It is also found in
KilA-N_domain
Protein family
domain, in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain as a new class of Zn-containing DNA-binding domain with
GCM_transcription_factors
Protein-coding gene in the species Homo sapiens
Z-DNA-binding protein 1 (also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1) is a mammalian intracellular protein that acts
ZBP1
Protein domain
one or two WRKY protein domains. The WRKY protein domain is 60 to 70 amino acids long type of DNA binding domain. The domain is characterized by a highly
WRKY_protein_domain
Protein structural motif
with one helix containing basic amino acid residues that facilitate DNA binding. In general, one helix is smaller, and due to the flexibility of this
Basic_helix–loop–helix
DNA-binding motif
The AT-hook is a DNA-binding motif present in many proteins, including the high-mobility group (HMG) proteins, DNA-binding proteins from plants and hBRG1
AT-hook
Protein family
glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal
GATA_zinc_finger
Protein
DnaA binding to 9-mer (9-bp) repeats upstream of oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to
DnaA
Protein domain
N-terminus they contain a dtxR-type HTH domain. This is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 amino acids present in metalloregulators
Iron_dependent_repressor
Self-stable region of a protein's chain that folds independently from the rest
phosphotyrosine binding domain of the src viral oncogene, which is itself a tyrosine kinase. See also: SH3 domain. Zinc finger DNA-binding domain (ZnF_GATA):
Protein_domain
Protein family
as a Q-linker. The C-Terminal domain, also known as the DNA Binding Domain (DBD), shows high affinity for regions in DNA that are rich in Adenine and Thymine
Histone-like nucleoid-structuring protein
Histone-like_nucleoid-structuring_protein
Drugs acting on the estrogen receptor
sequence identity in the DNA-binding domain and about 56% in the ligand-binding domain. The main difference of the ligand-binding domains is determined by Leu-384
Selective estrogen receptor modulator
Selective_estrogen_receptor_modulator
Protein-coding gene in the species Homo sapiens
transcription factor with multiple DNA binding domains (CUT1, CUT2 and a Homeobox domain). SATB1 specifically binds to AT-rich DNA sequences with high unwinding
SATB1
Protein-coding gene in the species Homo sapiens
sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. In cancer
GCM1
Medical condition
functional domains: the transactivation domain (also called the transcription-regulation domain or the NH2-terminal domain), the DNA-binding domain, the hinge
Androgen insensitivity syndrome
Androgen_insensitivity_syndrome
Transcription factor
fold-domain containing transcription factors (fork head box (FOX) and NF-Y) and other transcription factors that use zinc finger(s) for DNA binding (Groucho
Pioneer_factor
Topics referred to by the same term
initiative Dielectric barrier discharge, a type of electrical discharge DNA-binding domain, a protein motif DataBase Driver, a plug-in module for Perl DBI dB(D)
DBD
Type of protein
various structural motifs, such as RNA recognition motif (RRM), dsRNA binding domain, zinc finger and others. They are cytoplasmic and nuclear proteins.
RNA-binding_protein
Protein which mediates cellular response in two-component regulatory systems
features of effector domains: regulators with a DNA-binding effector domain, regulators with an enzymatic effector domain, and single-domain response regulators
Response_regulator
Region within a prokaryotic cell containing genetic material
domain. This is evident in the DNA binding of MatP and MukB in the Ter domain. DNA binding of MatP is enriched in the Ter domain, whereas DNA binding
Nucleoid
Protein-coding gene in the species Homo sapiens
that contains three domains, a DNA binding domain, an adenylation domain and an oligonucleotide / oligosaccharide binding-fold domain. When these enzymes
DNA_ligase_3
Transcription factor
known as Dehydration Response Element Binding factors (DREBs), they are a subfamily of AP2 DNA-binding domain transcription factors. Mutation studies
C-Repeat_Binding_Factor
Transcription factor gene of the forkhead box family
of transcription factors, proteins that regulate gene expression by binding to DNA. It is expressed in the brain, heart, lungs and digestive system. FOXP2
FOXP2
DNA pattern affecting anatomy development
that this gene contained a 180 base pair sequence that encoded a DNA binding domain, which William McGinnis termed the "homeobox". The existence of additional
Homeobox
Receptor to which cortisol and other glucocorticoids bind
following domains (labeled A - F): A/B - N-terminal regulatory domain C - DNA-binding domain (DBD) D - hinge region E - ligand-binding domain (LBD) F -
Glucocorticoid_receptor
DNA-binding structural motif
eukaryotic transcription factors. The bZIP domain is 60 to 80 amino acids in length with a highly conserved DNA binding basic region and a more diversified leucine
Leucine_zipper
Bacteria use a variety of DNA-binding proteins, generally basic in pH. Since bacterial binding proteins have a diversity of functions, it has been difficult
Bacterial_DNA_binding_protein
Protein-coding gene in the species Homo sapiens
Non-POU domain-containing octamer-binding protein (NonO) is a protein that in humans is encoded by the NONO gene. The NonO protein belongs to the Drosophila
Non-POU domain-containing octamer-binding protein
Non-POU_domain-containing_octamer-binding_protein
expression of plant genes that aid bacterial infection. The TALE domain responsible for binding to DNA is known to have 1.5 to 33.5 short sequences that are repeated
Transcription activator-like effector
Transcription_activator-like_effector
Genes that affect limb and heart development
DNA-binding domain, generally comprising about a third of the entire protein that is both necessary and sufficient for sequence-specific DNA binding.
T-box
Protein domain
cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain. Human
BRCT_domain
Enzymes that catalyze DNA formation
the purine towards the minor groove. Relative to the shape of DNA polymerase's binding pocket, steric clashes occur between the purine and residues in
DNA_polymerase
of proteins that contains a unique DNA binding domain termed the ETS domain. The transcriptional activation domain of SAP1a resides within the C-terminal
SAP1a
Mammalian protein found in humans
modulates the DNA-binding activity of the central domain. Most cancer-associated mutations in TP53 occur in the DBD, impairing DNA binding and transcriptional
P53
Canadian scientist
(1996-03-08). "Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA". Cell. 84 (5): 791–800. doi:10
Aled_Edwards
Plant gene
conserved domains: the DNA binding domain, a helix-turn-helix motif buried inside a unique 7-helix fold and a Sterile Alpha Motif. It binds DNA as a dimer
LEAFY
Transcription factor scaffold domain
The transactivation domain or trans-activating domain (TAD) is a transcription factor scaffold domain which contains binding sites for other proteins such
Transactivation_domain
Class of proteins involved in regulation of transcription
contains a DNA binding domain that binds either to a DNA promoter site or a specific DNA regulatory sequence called an enhancer. Binding of the activator-coactivator
Coactivator_(genetics)
Nuclear protein that binds to CREB
transcription. Aka interferon response factor binding domain (IBiD) The nuclear receptor coactivator binding domain (NCBD) located at the c-terminus of CBP
CREB-binding_protein
Transcription factor
called Zincore, Zinc finger co-regulator, can bind directly to the DNA-binding domain of zinc finger proteins, shedding light on how zinc finger transcription
Zinc finger transcription factor
Zinc_finger_transcription_factor
Oligonucleotide-Binding Evaluation (UniPROBE) is database of DNA-binding proteins determined by protein-binding microarrays. Protein microarray DNA-binding domain Newburger
UniPROBE
Chromodomain helicase DNA-binding (CHD) proteins is a subfamily of ATP-dependent chromatin remodeling complexes (remodelers). All remodelers fall under
Chromodomain helicase DNA-binding (CHD) subfamily
Chromodomain_helicase_DNA-binding_(CHD)_subfamily
Protein-coding gene in the species Homo sapiens
The TATA-binding protein (TBP) is a general transcription factor that binds to a DNA sequence called the TATA box. This DNA sequence is found about 30
TATA-binding_protein
Class of enzymes that divide DNA
generated by fusing a natural or engineered DNA-binding domain to a nuclease domain (often the cleavage domain of the type IIS restriction enzyme FokI).
Restriction_enzyme
Mammalian protein found in humans
androgen receptor. The main function of the androgen receptor is as a DNA-binding transcription factor that regulates gene expression; however, the androgen
Androgen_receptor
Family of transcription factors
with DP1,2 provides a second DNA binding site, increasing E2F binding stability. Most E2F have a pocket protein binding domain. Pocket proteins such as pRB
E2F
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DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
DNA BINDING-DOMAIN
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