first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549  6 VEVRYFAAAVDASHCESEYLTVPLGATLADLRELILSRHGApMEPILRVSAYLVGDDLTRDLGRVIGGR-VDVLPPFAGG 84
Cdd:cd00754   1 VKVLYFARARELAGKSEEELELPAGTTVEELLEELAAKYPA-LAAILKSVRVAVNQEYVDDDTELKDGDeVAFIPPVSGG 79

ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins; MoaD, also termed molybdopterin synthase sulfur carrier subunit, or MPT synthase subunit 1, or MPT synthase small subunit, or molybdopterin-converting factor small subunit, or molybdopterin-converting factor subunit 1, is a conserved small sulfur carrier protein that has beta-grasp ubiquitin-like (Ubl) fold involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. MoaD is activated in an ATP-dependent manner by sulfurtransferases similar to the activation mechanism of ubiquitin-activating enzyme E1.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549  6 VEVRYFAAAVDASHCESEYLTVPLGATLADLRELILSRHGApMEPILRVSAYLVGDDLTRDLGRVIGGR-VDVLPPFAGG 84
Cdd:cd00754   1 VKVLYFARARELAGKSEEELELPAGTTVEELLEELAAKYPA-LAAILKSVRVAVNQEYVDDDTELKDGDeVAFIPPVSGG 79

ThiS family; ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalyzed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549   8 VRYFAAAVDASHCESEyltVPLGATLADLRELILSRHGAPMEpilRVSAYLVGDDLTRDLGRVI---GGRVDVLPPFAGG 84
Cdd:pfam02597  1 VLLNAELRELAGKDEE---LAEGATVAELLEALGLRYPELRE---RVAVAVNGEIVPRLWLDTPlkdGDEVAIIPPVGGG 74

MoaD family protein, archaeal; Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin]

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549   6 VEVRYFAAAVDASHCESEYLTVPlGATLADLRELILSRHGAPMEPILRVSAYLV--------GDDLTRDLGRVI--GGRV 75
Cdd:TIGR01687  1 VRVKYFATLRDITGKKSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVpnviilvnGRNVDWGLGTELkdGDVV 79

                 ....*....
gi 771562549  76 DVLPPFAGG 84
Cdd:TIGR01687 80 AIFPPVSGG 88

ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins; MoaD, also termed molybdopterin synthase sulfur carrier subunit, or MPT synthase subunit 1, or MPT synthase small subunit, or molybdopterin-converting factor small subunit, or molybdopterin-converting factor subunit 1, is a conserved small sulfur carrier protein that has beta-grasp ubiquitin-like (Ubl) fold involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. MoaD is activated in an ATP-dependent manner by sulfurtransferases similar to the activation mechanism of ubiquitin-activating enzyme E1.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549  6 VEVRYFAAAVDASHCESEYLTVPLGATLADLRELILSRHGApMEPILRVSAYLVGDDLTRDLGRVIGGR-VDVLPPFAGG 84
Cdd:cd00754   1 VKVLYFARARELAGKSEEELELPAGTTVEELLEELAAKYPA-LAAILKSVRVAVNQEYVDDDTELKDGDeVAFIPPVSGG 79

ubiquitin-like (Ubl) domain found in a group of small sulfide carrier proteins; Ubiquitin-like (Ubl) domain found in a group of small sulfide carrier proteins This family includes ThiS, MoaD, CysO, QbsE, and their homologs, which are structurally homologous to ubiquitin (Ub) and may function as the sulfide donor for the biosynthesis of thiamin, molybdopterin, cysteine, thioquinolobactin, and other sulfur-containing natural products. Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. Like Ub, small sulfide carrier proteins in this family are adenylated at a diglycyl C-terminus by specific activating proteins. The adenylated C-terminus is subsequently converted to a thiocarboxylate, serving as the sulfide source. Those activating proteins are diverse and show little sequence similarity. This family also includes the small archaeal modifier protein (SAMP), including SAMP1, SAMP2 and SAMP3, which are Ub-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon Haloferax volcanii. SAMP1 and SAMP2 are involved in sulfur transfer during molybdenum cofactor biosynthesis and tRNA thiolation much like MoaD and Urm1, respectively. They can form covalent conjugates with their protein targets through an isopeptide linkage via their C-terminal diglycine motif in a streamlined archaeal E1-dependent pathway. SAMP2 also forms homo-conjugates through the intermolecular isopeptide bond between the C-terminal Gly and the Lys58 side chain, a feature that likely resembles polyubiquitination. SAMP3 conjugates are dependent on the Ub-activating E1 enzyme homolog of archaea (UbaA) for synthesis and are cleaved by the JAMM/MPN+ domain metalloprotease HvJAMM1.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549  6 VEVRYFAAAVDAsHCESEYLTVPLGATLADLRELILSRHGAPMEPIL-------RVSAYLVGDDLTRDLGRVI---GGRV 75
Cdd:cd17040   1 VKVRLFGALREA-GAGEEEIEVEGGTTVRDLLDALSERYPGLFEALDedgelrpFILVFVNGRDVRLDDGLTPlkdGDEV 79

                ....*....
gi 771562549 76 DVLPPFAGG 84
Cdd:cd17040  80 DILPPVAGG 88

Molybdopterin synthase sulfur carrier subunit

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 771562549  4 TQVEVRYFAAAVDASHCESEYLTVPLGATLADLRELILSRHGApMEPILRVSAYLVGDDLTRDLGRVI-GGRVDVLPPFA 82
Cdd:PLN02799  2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS-LEEVRSCCVLALNEEYTTESAALKdGDELAIIPPIS 80

                ..
gi 771562549 83 GG 84
Cdd:PLN02799 81 GG 82