NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1955831016|ref|XP_038904601|]
View 

B3 domain-containing transcription repressor VAL2 isoform X3 [Benincasa hispida]

Protein Classification

B3 domain-containing protein( domain architecture ID 10178197)

B3 domain-containing protein with a cysteine-tryptophan (CW)-type zinc finger, similar to Arabidopsis thaliana B3 domain-containing transcription repressors VAL1 and VAL2, which are transcriptional repressors of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3

Gene Ontology:  GO:0008270|GO:0006355
PubMed:  18986826|14607086

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 289-390 7.34e-22

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


:

Pssm-ID: 197383  Cd Length: 98  Bit Score: 90.85  E-value: 7.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 289 PLFEKMLSASDAGRIGRLVVPKACAEAYFPPisqPEGLPIRIQDVKGKEWVFQFRFWPNNNsRMYVLEGVTPCIQSMQLQ 368
Cdd:cd10017     1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---KEGVEVTLEDPDGKKWTVKLKKRKNSG-RMVLSGGWKEFVRANGLK 76

                          90       100
                  ....*....|....*....|..
gi 1955831016 369 AGDTVTFSRMDPEGKLIMGFRK 390
Cdd:cd10017    77 EGDFLVFELDGRNSKFKVRIFR 98
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 567-609 2.38e-10

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


:

Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.55  E-value: 2.38e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1955831016 567 WAQCDDCSKWRRLPVDVL---LPSKWTCLENIwDQSRSSCSILEEL 609
Cdd:pfam07496   2 WVQCDSCLKWRRLPTEIDpyeLPEPWYCSMNP-DPKYNSCDAPEEI 46
 
Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 289-390 7.34e-22

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


Pssm-ID: 197383  Cd Length: 98  Bit Score: 90.85  E-value: 7.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 289 PLFEKMLSASDAGRIGRLVVPKACAEAYFPPisqPEGLPIRIQDVKGKEWVFQFRFWPNNNsRMYVLEGVTPCIQSMQLQ 368
Cdd:cd10017     1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---KEGVEVTLEDPDGKKWTVKLKKRKNSG-RMVLSGGWKEFVRANGLK 76

                          90       100
                  ....*....|....*....|..
gi 1955831016 369 AGDTVTFSRMDPEGKLIMGFRK 390
Cdd:cd10017    77 EGDFLVFELDGRNSKFKVRIFR 98
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 291-392 1.64e-17

B3 DNA binding domain; This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by.


Pssm-ID: 396783 [Multi-domain]  Cd Length: 101  Bit Score: 78.57  E-value: 1.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 291 FEKMLSASDAGRIGRLVVPKACAEAYFpPISQPEGLPIRIQDVKGKEWvfQFRFWPNNNSRMYVLE-GVTPCIQSMQLQA 369
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENS-GLPKRLSKEITLLDEHGKSW--TVKLRYRKKSGRYVLTgGWKEFVKANGLKA 77

                          90       100
                  ....*....|....*....|....
gi 1955831016 370 GDTVTFSRMDPE-GKLIMGFRKAS 392
Cdd:pfam02362  78 GDFLTFKLVGNSgFTPVVGIFRKS 101
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 291-390 3.58e-16

B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations.


Pssm-ID: 214977  Cd Length: 96  Bit Score: 74.64  E-value: 3.58e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016  291 FEKMLSASDAGRIGRLVVPKACAEAYFPPISQPEglpIRIQDVKGKEWVFQFRFWpnNNSRMYVLEGVTPCI-QSMQLQA 369
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKE---ITLLDPDGKSWKVKLKYR--GSSGMFLLTGGWKEFvKANGLKA 75

                           90       100
                   ....*....|....*....|.
gi 1955831016  370 GDTVTFSRMDPEGKLIMGFRK 390
Cdd:smart01019  76 GDSLTFELDGNGEFVVSIFRK 96
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 567-609 2.38e-10

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.55  E-value: 2.38e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1955831016 567 WAQCDDCSKWRRLPVDVL---LPSKWTCLENIwDQSRSSCSILEEL 609
Cdd:pfam07496   2 WVQCDSCLKWRRLPTEIDpyeLPEPWYCSMNP-DPKYNSCDAPEEI 46
 
Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 289-390 7.34e-22

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


Pssm-ID: 197383  Cd Length: 98  Bit Score: 90.85  E-value: 7.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 289 PLFEKMLSASDAGRIGRLVVPKACAEAYFPPisqPEGLPIRIQDVKGKEWVFQFRFWPNNNsRMYVLEGVTPCIQSMQLQ 368
Cdd:cd10017     1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---KEGVEVTLEDPDGKKWTVKLKKRKNSG-RMVLSGGWKEFVRANGLK 76

                          90       100
                  ....*....|....*....|..
gi 1955831016 369 AGDTVTFSRMDPEGKLIMGFRK 390
Cdd:cd10017    77 EGDFLVFELDGRNSKFKVRIFR 98
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 291-392 1.64e-17

B3 DNA binding domain; This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by.


Pssm-ID: 396783 [Multi-domain]  Cd Length: 101  Bit Score: 78.57  E-value: 1.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 291 FEKMLSASDAGRIGRLVVPKACAEAYFpPISQPEGLPIRIQDVKGKEWvfQFRFWPNNNSRMYVLE-GVTPCIQSMQLQA 369
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENS-GLPKRLSKEITLLDEHGKSW--TVKLRYRKKSGRYVLTgGWKEFVKANGLKA 77

                          90       100
                  ....*....|....*....|....
gi 1955831016 370 GDTVTFSRMDPE-GKLIMGFRKAS 392
Cdd:pfam02362  78 GDFLTFKLVGNSgFTPVVGIFRKS 101
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 291-390 3.58e-16

B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations.


Pssm-ID: 214977  Cd Length: 96  Bit Score: 74.64  E-value: 3.58e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016  291 FEKMLSASDAGRIGRLVVPKACAEAYFPPISQPEglpIRIQDVKGKEWVFQFRFWpnNNSRMYVLEGVTPCI-QSMQLQA 369
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKE---ITLLDPDGKSWKVKLKYR--GSSGMFLLTGGWKEFvKANGLKA 75

                           90       100
                   ....*....|....*....|.
gi 1955831016  370 GDTVTFSRMDPEGKLIMGFRK 390
Cdd:smart01019  76 GDSLTFELDGNGEFVVSIFRK 96
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 567-609 2.38e-10

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.55  E-value: 2.38e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1955831016 567 WAQCDDCSKWRRLPVDVL---LPSKWTCLENIwDQSRSSCSILEEL 609
Cdd:pfam07496   2 WVQCDSCLKWRRLPTEIDpyeLPEPWYCSMNP-DPKYNSCDAPEEI 46
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 290-377 2.06e-06

DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response.


Pssm-ID: 197381  Cd Length: 109  Bit Score: 47.24  E-value: 2.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955831016 290 LFEKMLSASDAGRIG----RLVVPKACAEAYFPPISQPEGLP----IRIQDVK-GKEWVFQFRFWPNNNSRMYVLEGVTP 360
Cdd:cd10015     2 VLIKRLSANDTGATGghqvGLYIPKGIVEKFPPSINHTREANpsifLTMHDISdCRDWEARAIFYNSNRNEKRLTRGGRG 81

                          90
                  ....*....|....*..
gi 1955831016 361 CIQSMQLQAGDTVTFSR 377
Cdd:cd10015    82 FVKQNPLNTGDLTLIAF 98
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH