Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1229789803 345 YRKNANQHWDSMKSYYHKATAAYAKGERNYASYLSEQGRAQNRQAQKADDKASHNIFIARN 405
Cdd:pfam08590   2 LRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1229789803 151 QQEAEQFLCSMLGDEceLSMAVVRDVLCQCGYDVEKALNVLLDL 194
Cdd:cd14365     1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTLLNL 42

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1229789803 345 YRKNANQHWDSMKSYYHKATAAYAKGERNYASYLSEQGRAQNRQAQKADDKASHNIFIARN 405
Cdd:pfam08590   2 LRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62

CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an N-terminal ATP-binding region that is responsible for the interaction with BCL-3 and p300/CBP. N4BP2 also functions as a 5'-polynucleotide kinase that can transfer a phosphate group to the 5' end of DNA and RNA substrates. Moreover, N4BP2 contains a C-terminal MutS-related domain that possesses nicking endonuclease activity and may play a role in DNA mismatch repair (MMR). This model corresponds to CUE domain in the N-terminus of N4BP2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1229789803 151 QQEAEQFLCSMLGDEceLSMAVVRDVLCQCGYDVEKALNVLLDL 194
Cdd:cd14365     1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTLLNL 42

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1229789803 345 YRKNANQHWDSMKSYYHKATAAYAKGERNYASYLSEQGRAQNRQAQKADDKASHNIFIARN 405
Cdd:pfam08590   2 LRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62

CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an N-terminal ATP-binding region that is responsible for the interaction with BCL-3 and p300/CBP. N4BP2 also functions as a 5'-polynucleotide kinase that can transfer a phosphate group to the 5' end of DNA and RNA substrates. Moreover, N4BP2 contains a C-terminal MutS-related domain that possesses nicking endonuclease activity and may play a role in DNA mismatch repair (MMR). This model corresponds to CUE domain in the N-terminus of N4BP2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1229789803 151 QQEAEQFLCSMLGDEceLSMAVVRDVLCQCGYDVEKALNVLLDL 194
Cdd:cd14365     1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTLLNL 42

CUE domain found in ubiquitin-binding CUE proteins; This family includes many coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domain containing proteins that are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. CUE domains form three-helix bundle structures and are distantly related to the ubiquitin-associated (UBA) domains which are widely occurring ubiquitin-binding motifs found in a broad range of cellular proteins in species ranging from yeast to human. The majority of family members contain one CUE domain, but some family members from fungi harbor two CUE domains.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1229789803 152 QEAEQFLCSMLGDeceLSMAVVRDVLCQCGYDVEKALNVLL 192
Cdd:cd14279     1 DEKLEQLQEMFPD---LDEEVLEDVLEANNGDVEAAIDALL 38