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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958   34 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDfsmqppAQEISVRDLHDNIWIFRHIYRGQPKRHLLTTGWSLFVSGKKLS 113
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLK------PKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1847824958  114 AGDSVLFMRDERQQLLLGIRRA 135
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958   34 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDfsmqppAQEISVRDLHDNIWIFRHIYRGQPKRHLLTTGWSLFVSGKKLS 113
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLK------PKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1847824958  114 AGDSVLFMRDERQQLLLGIRRA 135
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958  33 FFCKTLTASDTSTHGGFSVPRRAAEKIFPPldfsmqPPAQEISVRDLHDNIWIFRHIYRGQPKRHLLTTGWSLFVSGKKL 112
Cdd:cd10017     2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75

                          90
                  ....*....|...
gi 1847824958 113 SAGDSVLFMRDER 125
Cdd:cd10017    76 KEGDFLVFELDGR 88

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958 831 KVHKRGAVGRSIDIARYSGYDELKQDLARMFGIEGQLeghqrigWKLVYVDHENDVLLVGDDpwEEFVNCVRFIKILSPQ 910
Cdd:cd05992     4 KVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVS-------FKLKYPDEDGDLVTISSD--EDLEEAIEEARRSGSK 74

                  ...
gi 1847824958 911 EVQ 913
Cdd:cd05992    75 KLR 77

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958   34 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDfsmqppAQEISVRDLHDNIWIFRHIYRGQPKRHLLTTGWSLFVSGKKLS 113
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLK------PKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1847824958  114 AGDSVLFMRDERQQLLLGIRRA 135
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958  33 FFCKTLTASDTSTHGGFSVPRRAAEKIFPPldfsmqPPAQEISVRDLHDNIWIFRHIYRGQPKRHLLTTGWSLFVSGKKL 112
Cdd:cd10017     2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75

                          90
                  ....*....|...
gi 1847824958 113 SAGDSVLFMRDER 125
Cdd:cd10017    76 KEGDFLVFELDGR 88

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958  34 FCKTLTASDTSTHGG----FSVPRRAAEKIFPPLDFSMQ-PPAQEISVRDLHDN-IWIFRHIYRGQPK-RHLLTTGWSLF 106
Cdd:cd10015     3 LIKRLSANDTGATGGhqvgLYIPKGIVEKFPPSINHTREaNPSIFLTMHDISDCrDWEARAIFYNSNRnEKRLTRGGRGF 82

                          90
                  ....*....|....*..
gi 1847824958 107 VSGKKLSAGDSVLFMRD 123
Cdd:cd10015    83 VKQNPLNTGDLTLIAFD 99

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1847824958 831 KVHKRGAVGRSIDIARYSGYDELKQDLARMFGIEGQLeghqrigWKLVYVDHENDVLLVGDDpwEEFVNCVRFIKILSPQ 910
Cdd:cd05992     4 KVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVS-------FKLKYPDEDGDLVTISSD--EDLEEAIEEARRSGSK 74

                  ...
gi 1847824958 911 EVQ 913
Cdd:cd05992    75 KLR 77