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 215768497  66 VRYDGELDVHPRVAYLALNYVDRYLSKRQLACERnPWAPRLLAISCLTLAAKMQRAAAISAADIQ-RGEEFMFDEAKIQR 144
Cdd:cd20543   10 LKVRSRYGFGPLTAYLAVNYLDRFLSSYDLPKDK-PWMLQLLAVACLSLAAKMEETDVPLLVDLQvEEPKYVFEAKTIQR 88

                         90
                 ....*....|.
gi 215768497 145 MEQMVLNALEW 155
Cdd:cd20543   89 MELLVLSTLEW 99

first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  66 VRYDGELDVHPRVAYLALNYVDRYLSKRQLACERnPWAPRLLAISCLTLAAKMQRAAAISAADIQ-RGEEFMFDEAKIQR 144
Cdd:cd20543   10 LKVRSRYGFGPLTAYLAVNYLDRFLSSYDLPKDK-PWMLQLLAVACLSLAAKMEETDVPLLVDLQvEEPKYVFEAKTIQR 88

                         90
                 ....*....|.
gi 215768497 145 MEQMVLNALEW 155
Cdd:cd20543   89 MELLVLSTLEW 99

second cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497 160 VTPLAFLGFFLSaCFPQPRHpalLDAIKARAVDLLLRVQPEVKMAEFSPSVaaaaallaaageVAGA-------HLLGFE 232
Cdd:cd20544    1 VTPFSFLDYFIS-KIGLSDS---REELLSRATELLLSTTKDIRFLEYRPSV------------IAAAailcaldELPPDD 64

                         90       100
                 ....*....|....*....|....*.
gi 215768497 233 AGVAACP-----FVNSEKLRECGEVM 253
Cdd:cd20544   65 ADDASSRlslllSPNKEKVKKCYELM 90

Cyclin [Cell division and chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  80 YLALNYVDRYLSKRQLACERNpwapRLLAISCLTLAAKMQRAAAISAADIQRGEEFMFDEAKIQRMEQMVLNALEWRTRS 159
Cdd:COG5024  235 FLAINIIDRFLSSRVVSLEKY----QLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISW 310

                 ....*..
gi 215768497 160 VTPLAFL 166
Cdd:COG5024  311 PSPMSFL 317

first cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  66 VRYDGELDVHPRVAYLALNYVDRYLSKRQLACERnPWAPRLLAISCLTLAAKMQRAAAISAADIQ-RGEEFMFDEAKIQR 144
Cdd:cd20543   10 LKVRSRYGFGPLTAYLAVNYLDRFLSSYDLPKDK-PWMLQLLAVACLSLAAKMEETDVPLLVDLQvEEPKYVFEAKTIQR 88

                         90
                 ....*....|.
gi 215768497 145 MEQMVLNALEW 155
Cdd:cd20543   89 MELLVLSTLEW 99

second cyclin box found in plant cyclin-delta family; This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497 160 VTPLAFLGFFLSaCFPQPRHpalLDAIKARAVDLLLRVQPEVKMAEFSPSVaaaaallaaageVAGA-------HLLGFE 232
Cdd:cd20544    1 VTPFSFLDYFIS-KIGLSDS---REELLSRATELLLSTTKDIRFLEYRPSV------------IAAAailcaldELPPDD 64

                         90       100
                 ....*....|....*....|....*.
gi 215768497 233 AGVAACP-----FVNSEKLRECGEVM 253
Cdd:cd20544   65 ADDASSRlslllSPNKEKVKKCYELM 90

first cyclin box found in G1/S-specific cyclin-E (CCNE) family; The CCNE family includes two E-type cyclins, CCNE1 and CCNE2. CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form a serine/threonine kinase holoenzyme complexes. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  80 YLALNYVDRYLS------KRQLacernpwapRLLAISCLTLAAKMQRAAAISAADIQRGEEFMFDEAKIQRMEQMVLNAL 153
Cdd:cd20519   59 YLAVDFVDRYLStqtnvpKTQL---------QLIGITCLFIAAKLEEIYPPKLSEFAYVTDGACTEDEILTMELIILKAL 129

                 ..
gi 215768497 154 EW 155
Cdd:cd20519  130 NW 131

cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclin PCL1, PCL2 and similar proteins; The family includes a group of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinase, such as Saccharomyces cerevisiae G1/S-specific cyclin PCL1, PCL2, PCL9 and their vertebrate counterparts, cyclin Pas1/PHO80 domain-containing protein 1 (CNPPD1). PCL1 (also called PHO85 cyclin-1, or cyclin HCS26) and PCL2 (also called PHO85 cyclin-1, or cyclin HCS26 homolog) are G1/S-specific cyclin partners of the cyclin-dependent kinase (CDK) PHO85. They are essential for the control of the cell cycle at the G1/S (start) transition. The PCL1-PHO85 cyclin-CDK holoenzyme is involved in phosphorylation of the CDK inhibitor (CKI) SIC1, which is required for its ubiquitination and degradation, releasing repression of b-type cyclins and promoting exit from mitosis. Together with cyclin PCL2, it positively controls degradation of sphingoid long chain base kinase LCB4. PCL1-PHO85 also phosphorylates HMS1, NCP1 and NPA3, which may all have a role in mitotic exit. PCL2-PHO85 also phosphorylates RVS167, linking cyclin-CDK activity with organization of the actin cytoskeleton. PCL9 is an M/G1-specific cyclin partner of the cyclin-dependent kinase (CDK) PHO85. It may have a role in bud site selection in the G1 phase. The family also includes cyclin Pas1/PHO80 domain-containing protein 1 (CNPPD1) and similar proteins. Their biological functions remain unclear. Members of this family contain one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  73 DVHPRVAYLALNYVDRYLSKRQLACERNPWAPRLLAISCLTLAAKMQRAAAISAAdiQRGEEFMFDEAKIQRMEQMVLNA 152
Cdd:cd20557   14 RLSPSVVLLALVYLERLRRRLPEALLGQEGSPYRLFLVALMLASKYLDDESYSNK--SWAEISGLPVRELNAMEREFLEA 91

                 ...
gi 215768497 153 LEW 155
Cdd:cd20557   92 LDW 94

cyclin box found in cyclin-I (CCNI) and similar proteins; CCNI is an atypical cyclin because it is most abundant in post-mitotic cells. It is involved in various biological processes, such as cell survival, angiogenesis, cell differentiation, and cell cycle progression. CCNI contains a typical cyclin box near the N-terminus and a PEST sequence near the C-terminus. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  66 VRYDGEL----DVHPRVAYLALNYVDRYLSkrqlACERNPWAPRLLAISCLTLAAKMQRAAAI--SAADIQRGEEFMFDE 139
Cdd:cd20526    6 VRWLAELnsqfKFYPETFALAVSILDRFLA----SVKARPKYLRCIAISCLFLAAKTNEEDEVipSTKDLVRVSKCGCSV 81

                         90
                 ....*....|....*.
gi 215768497 140 AKIQRMEQMVLNALEW 155
Cdd:cd20526   82 AEVLRMERIILDKLHW 97

first cyclin box found in cyclin-B1 (CCNB1)-like family; The CCNB1-like family includes two B-type cyclins, CCNB1 and CCNB2, both of which are essential for the control of the cell cycle at the G2/M (mitosis) transition. Members in this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  73 DVH------PRVAYLALNYVDRYLSKRQLacernpwaPR----LLAISCLTLAAKMQRaaaISAADIqrgEEFMF--DEA 140
Cdd:cd20507   46 EVHlkfkllPETLYLTVNIIDRYLSKKQV--------PRkklqLVGVTALLIASKYEE---IYPPEI---KDFVYitDNA 111

                         90
                 ....*....|....*...
gi 215768497 141 ----KIQRMEQMVLNALE 154
Cdd:cd20507  112 ytreEILQMERDILKTLD 129

first cyclin box found in G1/S-specific cyclin-D1 (CCND1); CCND1, also called B-cell lymphoma 1 protein (BCL-1), or BCL-1 oncogene, or PRAD1 oncogene, is a regulatory component of the cyclin D1-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1. The complex also regulates the cell-cycle during G(1)/S transition. It is an important cell cycle regulatory protein involved in carcinogenesis of various human cancers. CCND1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  71 ELDVHPrvayLALNYVDRYLSKRQLACERnpwaPRLLAISCLTLAAKMQRAAAISAADIQRGEEFMFDEAKIQRMEQMVL 150
Cdd:cd20573   72 EEEVFP----LAMNYLDRFLSVEPTKKSR----LQLLGATCMFLASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLVL 143

                 ....*
gi 215768497 151 NALEW 155
Cdd:cd20573  144 NKLKW 148

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 215768497  71 ELDVHPRVAYLALNYVDRYLSKRQLACERnpwaPRLLAISCLTLAAKMQRaAAISAADIQrgEEFMFDEAKIQRMEQ 147
Cdd:cd00043   12 KLGLPEEVLELAIELLDRFLSKGLLLGRS----PELIAAACLYLACKLEE-LPRTLKEIA--KVSGVSEKELRKAEK 81

cyclin box found in Cyclin N-terminal domain-containing protein 2 (CNTD2) and similar proteins; CNTD2 is an atypical cyclin upregulated in human cancer tissues. It promotes cell proliferation and migration, as well as increases tumor growth in vivo. It can function as a prognostic factor and drug target. CNTD2 contains one cyclin box. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 215768497  80 YLALNYVDRYLSKRQLACERNpwapRLLAISCLTLAAKMQRAAAISAADIQRGEEFMFDEAKIQRMEQMVLNALEWR 156
Cdd:cd20542   23 HLAVALLDRYLSRQKISLSLL----QLLGITCLFIACKFEERFPPEVATLCYLTDDSYSKKQVLRMERRVLRRLRFD 95

first cyclin box found in Arabidopsis thaliana B-type cyclins (CycBs) and similar proteins; Plant B-type cyclins (CycBs) correspond to a group of G2/mitotic-specific cyclins that are functionally linked to S- and M-phases of the mitotic cycle, which predicts their involvement also in meiosis. CycBs associate with their partner cyclin-dependent kinases (CDKs) to trigger the kinase activity. They contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  72 LDVH------PRVAYLALNYVDRYLSKRQLAceRNPWapRLLAISCLTLAAKMQRaaaISAADIqrgEEFMF--DEA--- 140
Cdd:cd20567   62 IEVHlkfelmPETLYLTVNLIDRFLSVKQVP--RKEL--QLVGVTAMLIASKYEE---IWAPEV---NDFVYisDNAytr 131

                         90
                 ....*....|....*.
gi 215768497 141 -KIQRMEQMVLNALEW 155
Cdd:cd20567  132 kQILVMEKTMLNTLEF 147

first cyclin box found in G1/S-specific cyclin-D3 (CCND3) and similar proteins; CCND3 is a regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. In skeletal muscle, CCND3 plays a unique function in controlling the proliferation/differentiation balance of myogenic progenitor cells. CCND3 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215768497  81 LALNYVDRYLS-----KRQLacernpwapRLLAISCLTLAAKMQRAAAISAADIQRGEEFMFDEAKIQRMEQMVLNALEW 155
Cdd:cd20575   79 LAMNYVDRYLScvptrKAQL---------QLLGAVCMLLASKLRETTPLTIEKLCIYTDNSISPRQLLDWEILVLGKLKW 149