1UKV,2FOL,2RHD


Conserved Protein Domain Family
Rab1_Ypt1

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cd01869: Rab1_Ypt1 
Click on image for an interactive view with Cn3D
Rab GTPase family 1 includes the yeast homolog Ypt1
Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Statistics
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PSSM-Id: 206661
Aligned: 26 rows
Threshold Bit Score: 298.088
Created: 6-Jan-2012
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Conserved site includes 14 residues -Click on image for an interactive view with Cn3D
Feature 1:GTP/Mg2+ binding site [chemical binding site]
Evidence:
  • Comment:The active conformation of Rab is stabilized by interations between the gamma phosphate of GTP and two critically conserved residues, Thr in switch I and Gly in switch II
  • Structure:2FOL: Human Rab1a binds GDP and Mg2+, defined using 3.5 A contacts

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ######         #                                                     
1UKV_Y      7 YLFKLLLIGNSGVGKSCLLLRFSDDTYTn-dYISTIGVDFKIKTVELDGKTVKLQIWDTAGqERFRTITSSYYRGSHGII 85  baker's yeast
2FOL_A     24 YLFKLLLIGDSGVGKSCLLLRFADDTYTe-sYISTIGVDFKIRTIELDGKTIKLQIWDTAGqERFRTITSSYYRGAHGII 102 human
P16976      7 YLFKLLLIGDSSVGKSCFLLRFADDSYVd-sYISTIGVDFKIRTVEVEGKTVKLQIWDTAGqERFRTITSSYYRGAHGII 85  Zea mays
BAB40669    7 YLFKLLLIGDSGVGKSCLLLRFADDTYTd-tHIATIGVDFKIKTVQIDGKNVKLQIWDTAGqERFRTITSSYYRGAQGII 85  Entamoeba histolytica
CAF90455    2 YLFKLLLIGDSGVGKSCLLLRFADGAYTd-sYISTIGVDFKIRTVDMDGKTVKLQIWDTAGqERFRTITSSYYRGAHGIV 80  Tetraodon nigrovir...
AAP06156    7 YLFKLLLIGDSGVGKSCLLIRFADESFSe-tYISTIGVDFKIRTIDLDGKVVKLQIWDTAGqERFRTITSSYYRGAQGII 85  Schistosoma japonicum
XP_646027  32 MLLKILVIGDSGVGKSCMLLRFADNRFTd-sYISTIGVDFCIRTIELDGKKIKLQIWDTAGqERFKTITTSYYRGAHGLI 110 Dictyostelium disc...
AAP85297    6 YLFKIIIIGDSGAGKSSLLLRFADDTYSe-sYMSTIGVDFKIKTVKIDNVTIKLQIWDTAGqERFRTITSTYYRGAHGII 84  Babesia bovis
CAD98425   11 FLFKLVLIGDSGVGKSCLLLRFAQDDSFtdsYITTIGVDFRFRTIKIDDKIIKLQIWDTAGqERFRTITSAYYRGADGVV 90  Cryptosporidium pa...
CAB40900   11 YLYKIILIGDSGVGKSCILLRFSDDHFTe-sYITTIGVDFRFRTIKVDDKIVKLQIWDTAGqERFRTITSAYYRGADGII 89  malaria parasite P...
Feature 1                                         ## #                          ###           
1UKV_Y     86 IVYDVTDQESFNGVKM-WLQEIDRYAtSTVLKLLVGNKCDLKDKRVVEYDVAKEFADANKMPFLETSALDSTNVEDAFLT 164 baker's yeast
2FOL_A    103 VVYDVTDQESFNNVKQ-WLQEIDRYAsENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMT 181 human
P16976     86 IVYDITDMESFNNVKQ-WLDEIDRYAnDSVRKLLVGNKCDLAENRAVDTSVAQAYAQEVGIPFLETSAKESINVEEAFLA 164 Zea mays
BAB40669   86 VVYSVIDLQTFQNVRQ-WLQEIERYAsETVIKLLIGNKCDLDDERAVTVEQGQELANSLNVSFMEASAKKSLNVDELFIR 164 Entamoeba histolytica
CAF90455   81 LVYDVTEQASFDNVRL-WMDEIERYAcEDVSRLLVGNKSDLLAQKVVDAAAAQDLASCLKIPFLETSAKNSENVEKVFLT 159 Tetraodon nigrovir...
AAP06156   86 IVYDVTDKTSFINVKS-WLQEIEHYAnSTVNRLLVGNKCDLPKSRAVDTVDAMNFAKEHQMPFLETSAKEAINVEDAFME 164 Schistosoma japonicum
XP_646027 111 IVYDITSMDSFNSIKR-WLIDVDRFAsPSVLKLIVGNKCDLNSKRAVDFKIAKKFADELNIPIMETSAKESTAIDEAFIK 189 Dictyostelium disc...
AAP85297   85 TVYDVTSRVSFESVKKtWLVDIEKYSsANISKLLIGNKVDLEDSRAVTYDEAREFAEQNNMDYIEASAKTAQNVEKAFES 164 Babesia bovis
CAD98425   91 LVYDTTSTSSFDHIDE-WVTEVNRYT-TDSTKILIGNKCDLTSQKMVDFATGQKKAQELQVDFMESSAKNSTNVEECFVN 168 Cryptosporidium pa...
CAB40900   90 IIYDTTDRNSFLHIND-WMNEINKYTnEDTCKLLVGNKADCKDDIEITTMEGQNKAKELNISFIETSAKDATNVELAFTM 168 malaria parasite P...
Feature 1             
1UKV_Y    165 MARQIKES 172 baker's yeast
2FOL_A    182 MAAEIKKR 189 human
P16976    165 MSAAIKKS 172 Zea mays
BAB40669  165 IATDIMKN 172 Entamoeba histolytica
CAF90455  160 LASDIHRR 167 Tetraodon nigroviridis
AAP06156  165 MARQIKAS 172 Schistosoma japonicum
XP_646027 190 LASDIKKS 197 Dictyostelium discoideum AX4
AAP85297  165 IARALKDK 172 Babesia bovis
CAD98425  169 IARKLLEK 176 Cryptosporidium parvum
CAB40900  169 ITQELIKK 176 malaria parasite P. falciparum

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