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Conserved domains on  [gi|731421863|ref|XP_010661899|]
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histone H3-like centromeric protein CENH3 isoform X1 [Vitis vinifera]

Protein Classification

histone H3 family protein( domain architecture ID 19223538)

histone H3 family protein similar to histone H3-like centromeric protein that is specifically found in centromeric nucleosomes

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0046982|GO:0030527
PubMed:  8121801|33155135

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 60-153 8.44e-54

histone-fold domain found in histone H3 and similar proteins; Histone H3 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.


:

Pssm-ID: 467036  Cd Length: 95  Bit Score: 165.02  E-value: 8.44e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  60 RYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVT 139
Cdd:cd22911    2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVT 81

                         90
                 ....*....|....
gi 731421863 140 LMKKDWELARRIGG 153
Cdd:cd22911   82 LMPKDMQLARRIRG 95
 
Name Accession Description Interval E-value
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 60-153 8.44e-54

histone-fold domain found in histone H3 and similar proteins; Histone H3 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.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 165.02  E-value: 8.44e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  60 RYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVT 139
Cdd:cd22911    2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVT 81

                         90
                 ....*....|....
gi 731421863 140 LMKKDWELARRIGG 153
Cdd:cd22911   82 LMPKDMQLARRIRG 95
PLN00161 PLN00161
histone H3; Provisional
 35-153 3.79e-48

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 152.08  E-value: 3.79e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  35 PRRPTRTATDASPSTAGSQGQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQ 114
Cdd:PLN00161   9 RFRKGKKPQKEASGVTRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQ 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 731421863 115 EAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRIGG 153
Cdd:PLN00161  89 EATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
H3 smart00428
Histone H3;
54-153 4.31e-43

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 138.35  E-value: 4.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863    54 GQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEIS-RWTAEALVALQEAAEDYLVHLFEDAMLCA 132
Cdd:smart00428   2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDlRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81

                           90       100
                   ....*....|....*....|.
gi 731421863   133 IHAKRVTLMKKDWELARRIGG 153
Cdd:smart00428  82 IHAKRVTIMPKDIQLARRIRG 102
Histone pfam00125
Core histone H2A/H2B/H3/H4;
33-151 4.56e-37

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 123.70  E-value: 4.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863   33 APPRRPTRTATDASPSTAGSQGQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEIsRWTAEALVA 112
Cdd:pfam00125   8 ANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDL-RISADAVVA 86

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 731421863  113 LQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRI 151
Cdd:pfam00125  87 LQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
82-151 1.22e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 35.58  E-value: 1.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  82 IPAAPFIRTVREISyffapeISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRI 151
Cdd:COG2036    2 LPVAPVDRIIKKAG------AERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 60-153 8.44e-54

histone-fold domain found in histone H3 and similar proteins; Histone H3 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.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 165.02  E-value: 8.44e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  60 RYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVT 139
Cdd:cd22911    2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVT 81

                         90
                 ....*....|....
gi 731421863 140 LMKKDWELARRIGG 153
Cdd:cd22911   82 LMPKDMQLARRIRG 95
PLN00161 PLN00161
histone H3; Provisional
 35-153 3.79e-48

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 152.08  E-value: 3.79e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  35 PRRPTRTATDASPSTAGSQGQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQ 114
Cdd:PLN00161   9 RFRKGKKPQKEASGVTRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQ 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 731421863 115 EAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRIGG 153
Cdd:PLN00161  89 EATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
H3 smart00428
Histone H3;
54-153 4.31e-43

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 138.35  E-value: 4.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863    54 GQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEIS-RWTAEALVALQEAAEDYLVHLFEDAMLCA 132
Cdd:smart00428   2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDlRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81

                           90       100
                   ....*....|....*....|.
gi 731421863   133 IHAKRVTLMKKDWELARRIGG 153
Cdd:smart00428  82 IHAKRVTIMPKDIQLARRIRG 102
PTZ00018 PTZ00018
histone H3; Provisional
 1-154 5.60e-42

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 136.57  E-value: 5.60e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863   1 MTRTKHLARKSrnrrrqfaatpaspasagpSSAPPRRPTRTATDASPSTAGSQGQRKPFRYRPGTVALREIRRFQKTTHL 80
Cdd:PTZ00018   1 MARTKQTARKS-------------------TGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTEL 61

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 731421863  81 LIPAAPFIRTVREISYFFAPEIsRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRIGGK 154
Cdd:PTZ00018  62 LIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134
PLN00121 PLN00121
histone H3; Provisional
 1-154 1.24e-37

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 125.55  E-value: 1.24e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863   1 MTRTKHLARKSrnrrrqfaatpaspasAGPSSAPPRRPTRTATDASPSTAGSqgqRKPFRYRPGTVALREIRRFQKTTHL 80
Cdd:PLN00121   1 MARTKQTARKS----------------TGGKAPRKQLATKAARKSAPATGGV---KKPHRYRPGTVALREIRKYQKSTEL 61

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 731421863  81 LIPAAPFIRTVREISYFFAPEIsRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRIGGK 154
Cdd:PLN00121  62 LIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134
Histone pfam00125
Core histone H2A/H2B/H3/H4;
33-151 4.56e-37

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 123.70  E-value: 4.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863   33 APPRRPTRTATDASPSTAGSQGQRKPFRYRPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEIsRWTAEALVA 112
Cdd:pfam00125   8 ANPRRGGTAPEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDL-RISADAVVA 86

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 731421863  113 LQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRI 151
Cdd:pfam00125  87 LQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
PLN00160 PLN00160
histone H3; Provisional
 62-153 1.81e-30

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 105.90  E-value: 1.81e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  62 RPGTVALREIRRFQKTTHLLIPAAPFIRTVREISYFFAPEISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLM 141
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81

                         90
                 ....*....|..
gi 731421863 142 KKDWELARRIGG 153
Cdd:PLN00160  82 PKDMQLARRIRG 93
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 82-150 3.94e-05

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: 39.45  E-value: 3.94e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 731421863  82 IPAAPFIRTVREISyffapeISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARR 150
Cdd:cd22909    2 LPKAPVKRIIKKAG------AERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 102-148 1.73e-04

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: 37.97  E-value: 1.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 731421863 102 ISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELA 148
Cdd:cd00076   15 FDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
82-151 1.22e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 35.58  E-value: 1.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731421863  82 IPAAPFIRTVREISyffapeISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARRI 151
Cdd:COG2036    2 LPVAPVDRIIKKAG------AERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 100-150 4.58e-03

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: 34.41  E-value: 4.58e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 731421863 100 PEISRWTAEALVALQEAAEDYLVHLFEDAMLCAIHAKRVTLMKKDWELARR 150
Cdd:cd22929   17 PDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIK 67
 
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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