UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 214830451  295 EAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 356
Cdd:pfam16577   1 EAALYPHLPPDADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62

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
                 ....*....|....*...
gi 214830451   1 MAMSYVKDDIFRIYIKEK 18
Cdd:cd06402   70 MALGSLNDDTFRIYIKEK 87

UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 214830451  295 EAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 356
Cdd:pfam16577   1 EAALYPHLPPDADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62

UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role connected to the ubiquitin-proteasome pathway. It functions as a scaffolding protein that regulates a diverse range of signaling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors. It also plays a novel role in connecting receptor signals with the endosomal signaling network required for mediating TrkA-induced differentiation. SQSTM contains a PB1 dimerization domain, a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding site, and a C-terminal ubiquitin-associated (UBA) domain that mediates the recognition of polyubiquitin chains and ubiquitylated substrates.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 214830451 309 RLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ 348
Cdd:cd14320    1 KIEEALSQMLAMGFSNEGGWLTRLLEAKNGDIGKVLDVIQ 40

Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 214830451   39 HPNVICDGC-NGPVVGTRYKCSVCPDYDLCSVCEGKGLHRGH 79
Cdd:pfam00569   2 HKVYTCNGCsNDPSIGVRYHCLRCSDYDLCQSCFQTHKGGNH 43

The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, 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 noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

                         10
                 ....*....|....*...
gi 214830451   1 MAMSYVKDDIFRIYIKEK 18
Cdd:cd06402   70 MALGSLNDDTFRIYIKEK 87

UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 214830451  295 EAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 356
Cdd:pfam16577   1 EAALYPHLPPDADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62

UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role connected to the ubiquitin-proteasome pathway. It functions as a scaffolding protein that regulates a diverse range of signaling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors. It also plays a novel role in connecting receptor signals with the endosomal signaling network required for mediating TrkA-induced differentiation. SQSTM contains a PB1 dimerization domain, a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding site, and a C-terminal ubiquitin-associated (UBA) domain that mediates the recognition of polyubiquitin chains and ubiquitylated substrates.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 214830451 309 RLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ 348
Cdd:cd14320    1 KIEEALSQMLAMGFSNEGGWLTRLLEAKNGDIGKVLDVIQ 40

Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 214830451  42 VICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGlHRGHTK 81
Cdd:cd02249    1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKG-KKGHPP 39

Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 214830451   39 HPNVICDGC-NGPVVGTRYKCSVCPDYDLCSVCEGKGLHRGH 79
Cdd:pfam00569   2 HKVYTCNGCsNDPSIGVRYHCLRCSDYDLCQSCFQTHKGGNH 43

Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 214830451  44 CDGCNGpVVGTRYKCSVCPDYDLCSVC-EGKGLHRGHTKL 82
Cdd:cd02337    3 CNECKH-HVETRWHCTVCEDYDLCITCyNTKNHPHKMEKL 41

Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.

                         10        20        30
                 ....*....|....*....|....*....|
gi 214830451  42 VICDGCNG-PVVGTRYKCSVCPDYDLCSVC 70
Cdd:cd02344    1 VTCDGCQMfPINGPRFKCRNCDDFDFCENC 30

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 214830451   310 LIESLSQMLSMGFSDEggWLTRLLQTKNYDIGAALDTI 347
Cdd:smart00165   1 DEEKIDQLLEMGFSRE--EALKALRAANGNVERAAEYL 36

Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 214830451  42 VICDGCNG-PVVGTRYKCSVCPDYDLCSVCEGKGLHRGHTKLAFP 85
Cdd:cd02334    1 AKCNICKEfPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHP 45

Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 214830451  44 CDGCN-GPVVGTRYKCSVCPDYDLCSVCEGKG 74
Cdd:cd02345    3 CSACRkQDISGIRFPCQVCRDYSLCLGCYTKG 34