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Conserved domains on  [gi|499173584|ref|WP_010871171|]
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DNA-binding protein HmvA [Methanocaldococcus jannaschii]

Protein Classification

histone family protein( domain architecture ID 10005217)

histone family protein may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils; similar to Methanothermus fervidus histone Hmf-2 and Saccharomyces cerevisiae Hap3 (a histone-like subunit of the CCAAT-binding complex)

Gene Ontology:  GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
1-65 4.67e-19

Archaeal histone H3/H4 [Chromatin structure and dynamics];


:

Pssm-ID: 441639  Cd Length: 67  Bit Score: 73.71  E-value: 4.67e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQCDDE 65
Cdd:COG2036   1 ELPVAPVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
1-65 4.67e-19

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 73.71  E-value: 4.67e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQCDDE 65
Cdd:COG2036   1 ELPVAPVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 1-62 1.63e-17

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 69.49  E-value: 1.63e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:cd22909   1 ELPKAPVKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELA 62
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 2-62 1.19e-07

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 44.52  E-value: 1.19e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584   2 LPKATVKRIMKQHTDF-NISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:pfam00808  3 LPIARVKRIMKSDPDAgRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQA 64
 
Name Accession Description Interval E-value
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
1-65 4.67e-19

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 73.71  E-value: 4.67e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQCDDE 65
Cdd:COG2036   1 ELPVAPVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 1-62 1.63e-17

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 69.49  E-value: 1.63e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:cd22909   1 ELPKAPVKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELA 62
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 2-62 4.13e-08

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 45.67  E-value: 4.13e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499173584  2 LPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:cd00076   1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 2-62 1.19e-07

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 44.52  E-value: 1.19e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584   2 LPKATVKRIMKQHTDF-NISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:pfam00808  3 LPIARVKRIMKSDPDAgRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQA 64
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 2-62 4.25e-07

histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin.


Pssm-ID: 467054 [Multi-domain]  Cd Length: 79  Bit Score: 43.27  E-value: 4.25e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584  2 LPKATVKRIMKQHTDFN-ISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
Cdd:cd22929   4 LPLSRVKRIMKLDPDVTlVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAA 65
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 7-60 1.30e-05

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 39.81  E-value: 1.30e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 499173584  7 VKRIMKQ-HTDFNISAEAVDELCNMLEEII-KITTEvAEQNARKEGRKTIKARDIK 60
Cdd:cd22910  13 IYKVLKQvHPDLGISSKAMDIMNSFVNDIFeRIATE-ASRLARYNKRSTLTSRDIQ 67
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 2-59 1.61e-05

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


Pssm-ID: 467032  Cd Length: 91  Bit Score: 39.46  E-value: 1.61e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584  2 LPKATVKRIMKQHTDFN--ISAEAVD--ELCnmLEEIIKITTEVAEQNARKEGRKTIKARDI 59
Cdd:cd22907   8 LPIANIARIMKKALPPNakISKDAKEtmQEC--VSEFISFVTSEASERCQREKRKTITGDDI 67
HFD_Dpb3-like cd23645
histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) ...
 1-59 4.78e-05

histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) and similar proteins; Schizosaccharomyces pombe Dpb3 is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that is a heterotetramer consisting of cdc20/Pol2, Dpb2, Dpb3, and Dpb4, and participates in chromosomal DNA replication. Dpb3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. The Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation and H3K9 methylation in heterochromatin. The Dpb3-Dpb4 dimer is also required for the recruitment of sir2 to heterochromatin.


Pssm-ID: 467059 [Multi-domain]  Cd Length: 78  Bit Score: 37.98  E-value: 4.78e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499173584  1 MLPKATVKRIMKQHTDFNI-SAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDI 59
Cdd:cd23645   2 VLPLARVKRIIKADKDVKIcSKDAVFLISKATELFIEYLAEQAYELAKLEKRKTVQYKDL 61
HFD_CENP-W cd13732
histone-fold domain found in centromere protein W (CENP-W) and similar proteins; CENP-W, also ...
 3-69 1.84e-04

histone-fold domain found in centromere protein W (CENP-W) and similar proteins; CENP-W, also called cancer-up-regulated gene 2 protein (CUG2), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENP-A into centromeres. CENP-W is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENP-A. Moreover, CENP-W forms a heterodimer with CENP-T. This dimer co-assembles with CENP-S-CENP-X heterodimers at centromeres to form the tetrameric CENP-T-W-S-X complex, which is a subcomplex of the large constitutive centromere-associated network (CCAN, also known as the interphase centromere complex or ICEN). The heterotetrameric CENP-T-W-S-X complex binds and supercoils DNA and plays an important role in kinetochore assembly. CENP-W has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467029  Cd Length: 74  Bit Score: 36.43  E-value: 1.84e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499173584  3 PKATVKRIMKQHTDFNISAEAVDEL-----CNMLEEIIkittEVAEQNARKEGRKTIKARDIKQCDDERLKR 69
Cdd:cd13732   4 PRSTLKKIIKKHLPGLRLAKNADILvyldyLLFLQRLA----EEARTEARESGSKTIKPEHVRKAAKKVLKK 71
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 2-59 5.64e-04

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 35.57  E-value: 5.64e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499173584  2 LPKATVKRIMKQ--HTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDI 59
Cdd:cd22928   5 LPRAVITRIIKEalPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDV 64
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 1-60 9.85e-04

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 35.22  E-value: 9.85e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499173584  1 MLPKATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIK 60
Cdd:cd22920   2 SLPKSLVKKLFKHFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVE 61
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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