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3  structures 161  species 0  interactions 4019  sequences 61  architectures

Family: SBP (PF03110)

Summary: SBP domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Squamosa promoter binding protein". More...

Squamosa promoter binding protein Edit Wikipedia article

SBP
PDB 1ul4 EBI.jpg
Solution structure of the DNA-binding domain of Squamosa promoter binding protein-like 4
Identifiers
Symbol SBP
Pfam PF03110
InterPro IPR004333
PROSITE PDOC00798
SCOP 2lao
SUPERFAMILY 2lao
TCDB 3.A.1

The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.[1] SBP proteins are thought to be transcriptional activators.

Function

SPB proteins have roles in leaf development, vegetative phase change, flower and fruit development, plant architecture, sporogenesis, Gibberelic acid signaling and toxin response.[2]

Structure

The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands. The SBP domain is a highly conserved DNA-binding domain. It is approximately 80 amino acids in length and contains a zinc finger motif with two zinc-binding sites: Cys-Cys-His-Cys and Cys-Cys-Cys-His. It has a three-stranded antiparallel beta-sheet.[3]

References

  1. ^ Klein J, Saedler H, Huijser P (January 1996). "A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA". Mol. Gen. Genet. 250 (1): 7–16. PMID 8569690. doi:10.1007/bf02191820. 
  2. ^ Chen X, Zhang Z, Liu D, Zhang K, Li A, Mao L (2010). "SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development.". J Integr Plant Biol. 52 (11): 946–51. PMID 20977652. doi:10.1111/j.1744-7909.2010.00987.x. 
  3. ^ Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, et al. (2004). "A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.". J Mol Biol. 337 (1): 49–63. PMID 15001351. doi:10.1016/j.jmb.2004.01.015. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR004333


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SBP domain Provide feedback

SBP domains (for SQUAMOSA-pROMOTER BINDING PROTEIN) are found in plant proteins. It is a sequence specific DNA-binding domain [1]. Members of family probably function as transcription factors involved in the control of early flower development [1]. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.

Literature references

  1. Klein J, Saedler H, Huijser P; , Mol Gen Genet 1996;250:7-16.: A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. PUBMED:8569690 EPMC:8569690

  2. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S; , J Mol Biol 2004;337:49-63.: A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. PUBMED:15001351 EPMC:15001351


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004333

SBP (for SQUAMOSA-pROMOTER BINDING PROTEIN) domain is a sequence specific DNA-binding domain found in plant proteins [ PUBMED:8569690 ]. Members of family probably function as transcription factors involved in the control of early flower development [ PUBMED:8569690 ]. They share a highly conserved DNA-binding domain that contains two zinc-binding sites. Among the 11 possible ligands for the zinc atoms that are conserved in the SBP zinc finger, only 8 are used. The SBP zinc finger follows the general pattern C-x4-C-x16-C-x2-[HC]-x15-C-x2-C-x3-H-x11-C. Three other histidines are well conserved but not involved in zinc binding [ PUBMED:8569690 , PUBMED:15001351 ].

In vitro experiments show that the SBP zinc finger preferentially binds the consensus sequence -TNCGTACAA- [ PUBMED:10524240 ]. However, little is known of the physiological functions of these putative transcriptional regulators beyond their ability to bind DNA.

The solution structure of the SBP zinc finger has been solved [ PUBMED:15001351 ]. The first four Cys or His coordinate one zinc ion and the last four coordinate the other. It can be viewed as two structural subdomains, each subdomain containing a single zinc-binding pocket. The N-terminal subdomain consists of two short alpha helices whereas the C-terminal one contains a three-stranded antiparallel beta-sheet.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(75)
Full
(4019)
Representative proteomes UniProt
(6701)
RP15
(539)
RP35
(2300)
RP55
(3394)
RP75
(4418)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(75)
Full
(4019)
Representative proteomes UniProt
(6701)
RP15
(539)
RP35
(2300)
RP55
(3394)
RP75
(4418)
Alignment:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(75)
Full
(4019)
Representative proteomes UniProt
(6701)
RP15
(539)
RP35
(2300)
RP55
(3394)
RP75
(4418)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_737 (release 6.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 75
Number in full: 4019
Average length of the domain: 71.00 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 14.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.8 21.6
Noise cut-off 21.5 21.4
Model length: 75
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SBP domain has been found. There are 3 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096SVS6 View 3D Structure Click here
A0A0R0FJD6 View 3D Structure Click here
A0A0R0FW55 View 3D Structure Click here
A0A0R0HMP6 View 3D Structure Click here
A0A0R0L7L1 View 3D Structure Click here
A0A1B1MQB5 View 3D Structure Click here
A0A1D6DVJ6 View 3D Structure Click here
A0A1D6ESU3 View 3D Structure Click here
A0A1D6EWJ8 View 3D Structure Click here
A0A1D6FAL8 View 3D Structure Click here
A0A1D6FQB3 View 3D Structure Click here
A0A1D6G5U7 View 3D Structure Click here
A0A1D6GDW8 View 3D Structure Click here
A0A1D6H093 View 3D Structure Click here
A0A1D6H872 View 3D Structure Click here
A0A1D6I4K3 View 3D Structure Click here
A0A1D6I853 View 3D Structure Click here
A0A1D6ICF4 View 3D Structure Click here
A0A1D6IYZ6 View 3D Structure Click here
A0A1D6JD63 View 3D Structure Click here
A0A1D6KIX0 View 3D Structure Click here
A0A1D6KMW1 View 3D Structure Click here
A0A1D6LAD4 View 3D Structure Click here
A0A1D6LQH3 View 3D Structure Click here
A0A1D6MRH1 View 3D Structure Click here
A0A1D6N2V6 View 3D Structure Click here
A3A2Z8 View 3D Structure Click here
A3C057 View 3D Structure Click here
B4F8H7 View 3D Structure Click here
B4F9Z9 View 3D Structure Click here
B4FG20 View 3D Structure Click here
B4FLF0 View 3D Structure Click here
B4FXD9 View 3D Structure Click here
B6TF72 View 3D Structure Click here
B6TPH6 View 3D Structure Click here
B7ZYE2 View 3D Structure Click here
B9DI20 View 3D Structure Click here
C0P8B7 View 3D Structure Click here
C0P8S5 View 3D Structure Click here
C4JBI6 View 3D Structure Click here
I1JBB8 View 3D Structure Click here
I1JMV9 View 3D Structure Click here
I1K6N7 View 3D Structure Click here
I1KDS8 View 3D Structure Click here
I1KJN9 View 3D Structure Click here
I1KKM7 View 3D Structure Click here
I1KLM6 View 3D Structure Click here
I1L206 View 3D Structure Click here
I1LT75 View 3D Structure Click here
I1LV25 View 3D Structure Click here
I1M086 View 3D Structure Click here
I1M219 View 3D Structure Click here
I1M360 View 3D Structure Click here
I1M3R4 View 3D Structure Click here
I1MEK9 View 3D Structure Click here
I1MF88 View 3D Structure Click here
I1MHQ9 View 3D Structure Click here
I1N2A2 View 3D Structure Click here
I1N7U1 View 3D Structure Click here
I1N969 View 3D Structure Click here
I1ND03 View 3D Structure Click here
K7K0P9 View 3D Structure Click here
K7K2H7 View 3D Structure Click here
K7K2H8 View 3D Structure Click here
K7K7W5 View 3D Structure Click here
K7K967 View 3D Structure Click here
K7KEH7 View 3D Structure Click here
K7KF17 View 3D Structure Click here
K7KKE6 View 3D Structure Click here
K7KL73 View 3D Structure Click here
K7KVJ3 View 3D Structure Click here
K7KW87 View 3D Structure Click here
K7L1B4 View 3D Structure Click here
K7L3G6 View 3D Structure Click here
K7L4C4 View 3D Structure Click here
K7LNN2 View 3D Structure Click here
K7LRZ2 View 3D Structure Click here
K7M106 View 3D Structure Click here
K7MFC4 View 3D Structure Click here
K7MKJ4 View 3D Structure Click here
K7MP80 View 3D Structure Click here
K7TP97 View 3D Structure Click here
K7UCC7 View 3D Structure Click here
O04003 View 3D Structure Click here
P0DI11 View 3D Structure Click here
P93015 View 3D Structure Click here
Q0DAE8 View 3D Structure Click here
Q0E3F8 View 3D Structure Click here
Q0J0K1 View 3D Structure Click here
Q0JGI1 View 3D Structure Click here
Q2R3Y1 View 3D Structure Click here
Q49I55 View 3D Structure Click here
Q49I57 View 3D Structure Click here
Q5Z818 View 3D Structure Click here
Q653Z5 View 3D Structure Click here
Q6H509 View 3D Structure Click here
Q6I576 View 3D Structure Click here
Q6YZE8 View 3D Structure Click here
Q6Z461 View 3D Structure Click here
Q6Z8M8 View 3D Structure Click here
Q700C2 View 3D Structure Click here
Q700W2 View 3D Structure Click here
Q75LH6 View 3D Structure Click here
Q7EXZ2 View 3D Structure Click here
Q7XPY1 View 3D Structure Click here
Q7XT42 View 3D Structure Click here
Q8GXL3 View 3D Structure Click here
Q8RY95 View 3D Structure Click here
Q8S9G8 View 3D Structure Click here
Q8S9L0 View 3D Structure Click here
Q94JW8 View 3D Structure Click here
Q9FZK0 View 3D Structure Click here
Q9LGU7 View 3D Structure Click here
Q9M2Q6 View 3D Structure Click here
Q9S758 View 3D Structure Click here
Q9S7A9 View 3D Structure Click here
Q9S7P5 View 3D Structure Click here
Q9S840 View 3D Structure Click here
Q9SMX9 View 3D Structure Click here