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Conserved domains on  [gi|564970624|gb|AHC05832|]
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LEAFY-like protein, partial [Dendrobium equitans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
C_LFY_FLO super family cl38806
DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant ...
 196-344 6.73e-98

DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY, recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression. This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA.


The actual alignment was detected with superfamily member pfam17538:

Pssm-ID: 407531  Cd Length: 169  Bit Score: 286.89  E-value: 6.73e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564970624  196 SERSGAGERQREHPFIVTEPGEVARAKKNGLDYLFHLYEQCHEFLLQVQALAKERGDKCPTKVTNLVFRYAKKVGARYIN 275
Cdd:pfam17538   1 EGGSGGGERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCRNFLIQVQALAKERGEKCPTKVTNQVFRYAKKAGASYIN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564970624  276 KPKKRHYVHCYALHVLDEEASNALRRAFKERGENVGAWRLACYKPLVAISCAHAFDIDAVFNAHPRLSI 344
Cdd:pfam17538  81 KPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGAWRQACYHPLVAISARHGWDIDALFAAHPRLAI 149
SAM_LFY super family cl03318
Floricaula / Leafy protein SAM domain; This family consists of various plant development ...
 1-45 3.98e-23

Floricaula / Leafy protein SAM domain; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species.


The actual alignment was detected with superfamily member pfam01698:

Pssm-ID: 396318  Cd Length: 80  Bit Score: 91.35  E-value: 3.98e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 564970624    1 TLVGMREEEVDDMMATLSHLFRWDLLVGERYGIKAAIRAERRRSE 45
Cdd:pfam01698  32 TLVNMKEEELDDMMNSLSHIFRWDLLVGERYGIKAAIRAERRRLE 76
 
Name Accession Description Interval E-value
C_LFY_FLO pfam17538
DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant ...
 196-344 6.73e-98

DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY, recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression. This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA.


Pssm-ID: 407531  Cd Length: 169  Bit Score: 286.89  E-value: 6.73e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564970624  196 SERSGAGERQREHPFIVTEPGEVARAKKNGLDYLFHLYEQCHEFLLQVQALAKERGDKCPTKVTNLVFRYAKKVGARYIN 275
Cdd:pfam17538   1 EGGSGGGERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCRNFLIQVQALAKERGEKCPTKVTNQVFRYAKKAGASYIN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564970624  276 KPKKRHYVHCYALHVLDEEASNALRRAFKERGENVGAWRLACYKPLVAISCAHAFDIDAVFNAHPRLSI 344
Cdd:pfam17538  81 KPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGAWRQACYHPLVAISARHGWDIDALFAAHPRLAI 149
SAM_LFY pfam01698
Floricaula / Leafy protein SAM domain; This family consists of various plant development ...
 1-45 3.98e-23

Floricaula / Leafy protein SAM domain; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species.


Pssm-ID: 396318  Cd Length: 80  Bit Score: 91.35  E-value: 3.98e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 564970624    1 TLVGMREEEVDDMMATLSHLFRWDLLVGERYGIKAAIRAERRRSE 45
Cdd:pfam01698  32 TLVNMKEEELDDMMNSLSHIFRWDLLVGERYGIKAAIRAERRRLE 76
 
Name Accession Description Interval E-value
C_LFY_FLO pfam17538
DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant ...
 196-344 6.73e-98

DNA Binding Domain (C-terminal) Leafy/Floricaula; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY, recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression. This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA.


Pssm-ID: 407531  Cd Length: 169  Bit Score: 286.89  E-value: 6.73e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564970624  196 SERSGAGERQREHPFIVTEPGEVARAKKNGLDYLFHLYEQCHEFLLQVQALAKERGDKCPTKVTNLVFRYAKKVGARYIN 275
Cdd:pfam17538   1 EGGSGGGERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCRNFLIQVQALAKERGEKCPTKVTNQVFRYAKKAGASYIN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564970624  276 KPKKRHYVHCYALHVLDEEASNALRRAFKERGENVGAWRLACYKPLVAISCAHAFDIDAVFNAHPRLSI 344
Cdd:pfam17538  81 KPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGAWRQACYHPLVAISARHGWDIDALFAAHPRLAI 149
SAM_LFY pfam01698
Floricaula / Leafy protein SAM domain; This family consists of various plant development ...
 1-45 3.98e-23

Floricaula / Leafy protein SAM domain; This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species.


Pssm-ID: 396318  Cd Length: 80  Bit Score: 91.35  E-value: 3.98e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 564970624    1 TLVGMREEEVDDMMATLSHLFRWDLLVGERYGIKAAIRAERRRSE 45
Cdd:pfam01698  32 TLVNMKEEELDDMMNSLSHIFRWDLLVGERYGIKAAIRAERRRLE 76
 
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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