26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721   1 MVLESTMICFDNSDFQRNGDYFPTRLIVQRDGINLVCLTKLRSNPENNVGLMTLSN-TVEVLATLTSDAGRIFSKMHLVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGnSPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721  80 PKGEINLLTGIRIAHLVLKHRQGKNHKMRIVVFVGSPINHEEGDLVKQAKRLKKEKVNVDIVSFGDHGNNNEILTAFINA 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 17737721 160 LNGKDgtGSHLVSVPRGSVL-SDALLSSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLlSDALLSSP 187

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721   1 MVLESTMICFDNSDFQRNGDYFPTRLIVQRDGINLVCLTKLRSNPENNVGLMTLSN-TVEVLATLTSDAGRIFSKMHLVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGnSPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721  80 PKGEINLLTGIRIAHLVLKHRQGKNHKMRIVVFVGSPINHEEGDLVKQAKRLKKEKVNVDIVSFGDHGNNNEILTAFINA 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 17737721 160 LNGKDgtGSHLVSVPRGSVL-SDALLSSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLlSDALLSSP 187

RAZUL (Rpn10 AZUL-binding) domain of 26S proteasome non-ATPase regulatory subunit 4 (PSMD4) and similar proteins; PSMD4 is also called 26S proteasome regulatory subunit RPN10, 26S proteasome regulatory subunit S5A, antisecretory factor 1, AF, ASF, or multiubiquitin chain-binding protein (MCB1). It acts as a ubiquitin receptor subunit through ubiquitin-interacting motifs and selects ubiquitin-conjugates for destruction. It displays a preferred selectivity for longer polyubiquitin chains. PSMD4 is a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. The proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. The model corresponds to the C-terminal Rpn10 AZUL-binding domain (RAZUL) of PSMD4, which is responsible for binding the AZUL domain of E6AP/UBE3A. AZUL stands for amino-terminal zinc-binding domain of ubiquitin E3a ligase.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 17737721 341 DVDEDYSEVIGDPAFLQSVLENLPGVDPQSEAVRDAVGSL 380
Cdd:cd22297   1 SEEEDMSDVMQDPEFLQSVLGSLPGVDPNDEAVQNALGSL 40

vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and metabolism];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721  45 PENNVGLMTLSNTVEVLATLTSDAGRIFSKMHLVQPKGEINLLTGIRIAHLVLkhRQGKNHKMRIVVFV--GSPiNHEEG 122
Cdd:COG1240 127 PRDRVGLVAFGGEAEVLLPLTRDREALKRALDELPPGGGTPLGDALALALELL--KRADPARRKVIVLLtdGRD-NAGRI 203

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 17737721 123 DLVKQAKRLKKEKVNVDIVSFGDHGNNNEILTAFINALNGK 163
Cdd:COG1240 204 DPLEAAELAAAAGIRIYTIGVGTEAVDEGLLREIAEATGGR 244

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721   1 MVLESTMICFDNSDFQRNGDYFPTRLIVQRDGINLVCLTKLRSNPENNVGLMTLSN-TVEVLATLTSDAGRIFSKMHLVQ 79
Cdd:cd01452   1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGnSPEVLVTLTNDQGKILSKLHDVQ 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721  80 PKGEINLLTGIRIAHLVLKHRQGKNHKMRIVVFVGSPINHEEGDLVKQAKRLKKEKVNVDIVSFGDHGNNNEILTAFINA 159
Cdd:cd01452  81 PKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160

                       170       180
                ....*....|....*....|....*....
gi 17737721 160 LNGKDgtGSHLVSVPRGSVL-SDALLSSP 187
Cdd:cd01452 161 VNGKD--GSHLVSVPPGENLlSDALLSSP 187

RAZUL (Rpn10 AZUL-binding) domain of 26S proteasome non-ATPase regulatory subunit 4 (PSMD4) and similar proteins; PSMD4 is also called 26S proteasome regulatory subunit RPN10, 26S proteasome regulatory subunit S5A, antisecretory factor 1, AF, ASF, or multiubiquitin chain-binding protein (MCB1). It acts as a ubiquitin receptor subunit through ubiquitin-interacting motifs and selects ubiquitin-conjugates for destruction. It displays a preferred selectivity for longer polyubiquitin chains. PSMD4 is a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. The proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. The model corresponds to the C-terminal Rpn10 AZUL-binding domain (RAZUL) of PSMD4, which is responsible for binding the AZUL domain of E6AP/UBE3A. AZUL stands for amino-terminal zinc-binding domain of ubiquitin E3a ligase.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 17737721 341 DVDEDYSEVIGDPAFLQSVLENLPGVDPQSEAVRDAVGSL 380
Cdd:cd22297   1 SEEEDMSDVMQDPEFLQSVLGSLPGVDPNDEAVQNALGSL 40

Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721  23 PTRLIVQRDGINLVCLTKLRSNPENNVGLMTLSNTVEVLATLTSDAG-----RIFSKMHLvQPKGEINLLTGIRIAHLVL 97
Cdd:cd00198  15 GEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDkadllEAIDALKK-GLGGGTNIGAALRLALELL 93

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 17737721  98 KHRQGKNHKMRIVVFVGSPINHEEGDLVKQAKRLKKEKVNVDIVSFGDHGNNNEI 152
Cdd:cd00198  94 KSAKRPNARRVIILLTDGEPNDGPELLAEAARELRKLGITVYTIGIGDDANEDEL 148

Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17737721   7 MICFDNSDFQRNGDYFPTRLIVQRDGINLVCLTKLRSNPENNVGLMTLSNT-VEVLATLTSDAGR-IFSKMHLVQPKGEI 84
Cdd:cd01453   7 IIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGrAEKLTDLTGNPRKhIQALKTARECSGEP 86

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 17737721  85 NLLTGIRIAHLVLKHRQGKNHKmRIVVFVGSPINHEEGDLVKQAKRLKKEKVNVDIVS 142
Cdd:cd01453  87 SLQNGLEMALESLKHMPSHGSR-EVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIG 143