Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606    1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                         90
                 ....*....|.
gi 564394746 911 CYRTQPQARSQ 921
Cdd:cd20606   81 CYRTQPQASSS 91

N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1-4.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 696 PQPLVNA-----VPVQNVSGETVSVTPVPGQTLVTMATATVTANNGQTV--TI--PVQGIANENGGITFFPVQVNVGGQA 766
Cdd:cd22553  124 VQGQANAsnvlqNIAQIASGGNAVQLPLNNMTQTIPVQVPVSTANGQTVyqTIqvPIQAIQSGNAGGGNQALQAQVIPQL 203

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 564394746 767 qAVTGSIQPlsaQALAgSLSSQqvtGTTLQVPGPVAIQQ 805
Cdd:cd22553  204 -AQAAQLQP---QQLA-QVSSQ---GYIQQIPANASQQQ 234

cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606    1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                         90
                 ....*....|.
gi 564394746 911 CYRTQPQARSQ 921
Cdd:cd20606   81 CYRTQPQASSS 91

Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746  831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:pfam01857   1 SLNLFFRKVYHLAAVRLQDLCSRLDLSSDLREKIWTCFEHSLVHQTDLMKDRHLDQILLCAIYVICKVTKEELTFKEIMK 80

                          90
                  ....*....|.
gi 564394746  911 CYRTQPQARSQ 921
Cdd:pfam01857  81 CYRKQPQASSH 91

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 696 PQPLVNA-----VPVQNVSGETVSVTPVPGQTLVTMATATVTANNGQTV--TI--PVQGIANENGGITFFPVQVNVGGQA 766
Cdd:cd22553  124 VQGQANAsnvlqNIAQIASGGNAVQLPLNNMTQTIPVQVPVSTANGQTVyqTIqvPIQAIQSGNAGGGNQALQAQVIPQL 203

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 564394746 767 qAVTGSIQPlsaQALAgSLSSQqvtGTTLQVPGPVAIQQ 805
Cdd:cd22553  204 -AQAAQLQP---QQLA-QVSSQ---GYIQQIPANASQQQ 234

cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins; RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20606    1 SLSLFFRKVYHLASVRLRDLCAKLDISDELRKKIWTCFEYSLVHCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 80

                         90
                 ....*....|.
gi 564394746 911 CYRTQPQARSQ 921
Cdd:cd20606   81 CYRTQPQASSS 91

Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746  101 KGTAEGNYVSLTRILRCSEQSLIEFFNKMKKWEDMANLPPHFRERTERLERNFTVSAVIFKKYEPIFQDIFKYPQEEqpR 180
Cdd:pfam11934   1 DGTVEGNCVSLTRLLRACKLSIIDFFKKMKQWADMANLDWEFRLEIKELERNFSVTTVLFKKYKRIFNELFLSPPPK--E 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 564394746  181 QQRGRKQRRQPCTTSEIFHFCWVLFIYAKGNFPMISDDLVNSYHLLLCALDLVYGN 236
Cdd:pfam11934  79 PKRSKKSRPAPCSYSDLFEFGWLLFLAAKNEFPSISKDLVTSYHLLLCCLDLVYVN 134

cyclin box found in retinoblastoma-like protein 1 (RBL1) and similar proteins; RBL1, also called 107 kDa retinoblastoma-associated protein (p107), retinoblastoma-related protein 1 (RBR-1), or pRb1, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL1 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RBL1 probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL1 contains one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 825 RPRKTSSLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKS 904
Cdd:cd20605    1 KPKKTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFSLVHCTDLMKDRHLDQLLLCAFYIMAKVTKEERT 80

                         90
                 ....*....|....*..
gi 564394746 905 FQNIMRCYRTQPQARSQ 921
Cdd:cd20605   81 FQDIMKCYRNQPQANSH 97

cyclin box found in retinoblastoma-associated protein (RB) and similar proteins; RB, also called p105-Rb, pRb, or pp110, is a key regulator of entry into cell division and also acts as a tumor suppressor. It promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. It also acts as a transcription repressor of E2F1 target genes. RB is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. It recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RB contains one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746 831 SLSLFFRKVYYLAGVRLRDLCTKLDISDELRKKIWTCFEFSIVQCPELMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMR 910
Cdd:cd20599    2 SLSLFYKKVYRLAYLRLNTLCDLLLLHPDLEHRIWTCFEHCLQNRYELLKDRHLDQIMMCSMYGICKVKNKDLRFKTIVT 81

                         90
                 ....*....|.
gi 564394746 911 CYRTQPQARSQ 921
Cdd:cd20599   82 AYKDLPHASQE 92

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564394746   845 VRLRDLCTKLDISDELRKKIWTCFEFSIVQCPelMMDRHLDQLLMCAIYVMAKVTKEDKSFQNIMRCYR 913
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYK--FLKYSPSLIAAAALYLASKTEETPPWTKELVHYTG 67

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564394746  41 QIQQRFEELCSRLNMDEAARAEAWSSYRSMSESYTLEGNDLHWLACA-LYVACRKsvptvskgtaEGNYVSLTRILRCSE 119
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAAcLYLACKL----------EELPRTLKEIAKVSG 70

                         90
                 ....*....|..
gi 564394746 120 QSLIEFFNKMKK 131
Cdd:cd00043   71 VSEKELRKAEKE 82