cellulose synthase-interactive protein; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  136 HLVRK--VGLISLITDLLKNSSPKVRQ---KALGSLRFVAKNDNDNKNEIAAGDNIRTIVKFLNHGHSQEKEQAVSLLYE 210
Cdd:PLN03200   556 KLVRTadAATISQLTALLLGDLPESKVhvlDVLGHVLSVASLEDLVREGSAANDALRTLIQLLSSSKEETQEKAASVLAD 635

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  211 LSEYKP-LSEKIGSVSgAILILVGLSSSKVENLLTvdRAEKTLENLESCEKNVRQMAEngrlqpllrlllegssdtqlsm 289
Cdd:PLN03200   636 IFSSRQdLCESLATDE-IINPCIKLLTNNTEAVAT--QSARALAALSRSIKENRKVSY---------------------- 690

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002313844  290 aahlgelvlsndvkvlVAQTAGSTLVNIMKSGNREAREAALKAL-NQISSYDTSAKILIEAGILP 353
Cdd:PLN03200   691 ----------------AAEDAIKPLIKLAKSSSIEVAEQAVCALaNLLSDPEVAAEALAEDIILP 739

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002313844  22 YESFLCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSggrrlVCPVTNKELSSTEL 79
Cdd:cd16664     1 PEEFICPISLELMKDPVILATGQTYERAAIEKWLDSGNN-----TCPITGQPLTHTDL 53

cellulose synthase-interactive protein; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  136 HLVRK--VGLISLITDLLKNSSPKVRQ---KALGSLRFVAKNDNDNKNEIAAGDNIRTIVKFLNHGHSQEKEQAVSLLYE 210
Cdd:PLN03200   556 KLVRTadAATISQLTALLLGDLPESKVhvlDVLGHVLSVASLEDLVREGSAANDALRTLIQLLSSSKEETQEKAASVLAD 635

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  211 LSEYKP-LSEKIGSVSgAILILVGLSSSKVENLLTvdRAEKTLENLESCEKNVRQMAEngrlqpllrlllegssdtqlsm 289
Cdd:PLN03200   636 IFSSRQdLCESLATDE-IINPCIKLLTNNTEAVAT--QSARALAALSRSIKENRKVSY---------------------- 690

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002313844  290 aahlgelvlsndvkvlVAQTAGSTLVNIMKSGNREAREAALKAL-NQISSYDTSAKILIEAGILP 353
Cdd:PLN03200   691 ----------------AAEDAIKPLIKLAKSSSIEVAEQAVCALaNLLSDPEVAAEALAEDIILP 739

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002313844  22 YESFLCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSggrrlVCPVTNKELSSTEL 79
Cdd:cd16664     1 PEEFICPISLELMKDPVILATGQTYERAAIEKWLDSGNN-----TCPITGQPLTHTDL 53

U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002313844  25 FLCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSggrrlvCPVTNKEL 74
Cdd:cd16453     1 FLCPISGELMKDPVITPSGITYDRSAIERWLLSDNT------DPFTREPL 44

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002313844  21 IYESFLCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSggrrlVCPVTNKELSSTELNPSIALRNTIDEWMHRNE 97
Cdd:pfam04564   1 IPDEFLDPITFELMTDPVILPSGITYDRSTIERHLLSVDP-----TDPFTREPLTHDQLIPNLELKAKIDAWLEEKR 72

SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Moreover, NSE2 together with its partner proteins SMC6 and SMC5 form a tight subcomplex of the structural maintenance of chromosomes SMC5-6 complex, which includes another two subcomplexes, NSE1-NSE3-NSE4 and NSE5-NSE6. SMC6 and NSE3 are sumoylated in an NSE2-dependent manner, but SMC5 and NSE1 are not. NSE2-dependent E3 SUMO ligase activity is required for efficient DNA repair, but not for SMC5-6 complex stability. NSE2 contains a RING variant known as a Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription)-like RING (SPL-RING) finger that is likely shared by the SP-RING type SUMO E3 ligases, such as PIAS family proteins. The SPL-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It harbors only one Zn binding site and is required for the sumoylating activity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  25 FLCPLSKQVMRDPVTIES-GATFEREAILKWFKDNGSGGRrlvCPVT--NKELSSTELNPSIALRNTIDE 91
Cdd:cd16651     1 LKCPITQQLMVDPVRNKKcGHTYEKAAILQYLQSRKKKAK---CPVAgcRNTVSKSDLVPDPELKRRIER 67

first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the first one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1002313844  25 FLCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSGgrrlvcPVTNKELSSTELNP 81
Cdd:cd23149     1 FTCPITSGFMEDPVITPSGFSYERSAIERWLETKPED------PQTREPLTAKDLQP 51

SP-RING finger and SPL-RING finger, variants of RING fingers; This family corresponds to a group of proteins with variants of RING fingers that are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. They include SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases and SPL-RING finger found in E3 SUMO-protein ligase NSE2. The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. The PIAS (protein inhibitor of activated STAT) protein family modulates the activity of several transcription factors and acts as an E3 ubiquitin ligase in the sumoylation pathway. NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1002313844  25 FLCPLSKQVMRDPVTIES-GATFEREAILKWFKdngSGGRRLVCPV 69
Cdd:cd16452     1 LKCPITQKRMKDPVRGKHcGHCFDLEAILQYLK---RRKKKWKCPV 43

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002313844  22 YEsflCPLSKQVMRDPVTIESGATFEREAILKWFKDNGSGgrrlvCPVTNKELSSTELNP 81
Cdd:cd16643     2 YE---CPICLMALREPVQTPCGHRFCKACILKSIREAGHK-----CPVDNEPLLENQLFP 53

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1002313844  25 FLCPLSKQVMRDPVTIESGATFEREAILKWFKD-NGSggrrLVCPV 69
Cdd:cd16601     2 ASCSLCKEYLKDPVIIECGHNFCRACITRFWEElDGD----FPCPQ 43

U-box domain 1, a modified RING finger, found in nitric oxide synthase-interacting protein (NOSIP) and similar proteins; NOSIP, also known as endothelial NO synthase (eNOS)-interacting protein, p33RUL, is an E3 ubiquitin-protein ligase implicated in the control of airway and vascular diameter, mucosal secretion, NO synthesis in ciliated epithelium, and, therefore, of mucociliary and bronchial function. The loss of NOSIP may cause holoprosencephaly and facial anomalies, including cleft lip/palate, cyclopia, and facial midline clefting. NOSIP interacts with neuronal nitric oxide synthase (nNOS) and eNOS by inhibiting the nitric oxide (NO) production. It acts as a novel type of modulator that promotes translocation of eNOS from the plasma membrane to intracellular sites, thereby uncoupling eNOS from plasma membrane caveolae and inhibiting NO synthesis. NOSIP also interacts with protein phosphatase PP2A and mediates the monoubiquitination of the PP2A catalytic subunit. Thus, it is a critical modulator of brain and craniofacial development in mice and a candidate gene for holoprosencephaly in humans. Moreover, NOSIP associates with the erythropoietin (Epo) receptor (EpoR), mediates ubiquitination of EpoR, and plays an essential role in erythropoietin-induced proliferation. NOSIP contains an atypical N-terminal RING-like U-box domain that is split into two parts by an interjacent stretch of 104 amino acid residues, as well as a C-terminal RING-like U-box domain. This model corresponds to the first U-box domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002313844  27 CPLSKQVMRDPVTIESGATFEREAILKWFKDngsggRRLVCPVTNKEL 74
Cdd:cd16661     4 CCLTLQPCRDPVVTPDGYLYDKEAILEYILH-----QKKECPMSGKPL 46

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002313844  25 FLCPLSKQVMRDPVTIESGATFEREAILKWFKdngsggRRLVCPVTNKEL 74
Cdd:cd16547     4 LICSICHGVLRCPVRLSCSHIFCKKCILQWLK------RQETCPCCRKEV 47