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
View PSSM: cd01869
Aligned: 26 rows
Threshold Bit Score: 298.088
Threshold Setting Gi: 32398960
Created: 6-Jan-2012
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
  next features
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
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                # ######         #                                                     
1UKV_Y        7 YLFKLLLIGNSGVGKSCLLLRFSDDTYTn-dYISTIGVDFKIKTVELDGKTVKLQIWDTAGqERFRTITSSYYRGSHGII 85
2FOL_A       24 YLFKLLLIGDSGVGKSCLLLRFADDTYTe-sYISTIGVDFKIRTIELDGKTIKLQIWDTAGqERFRTITSSYYRGAHGII 102
gi 466170     7 YLFKLLLIGDSSVGKSCFLLRFADDSYVd-sYISTIGVDFKIRTVEVEGKTVKLQIWDTAGqERFRTITSSYYRGAHGII 85
gi 13537429   7 YLFKLLLIGDSGVGKSCLLLRFADDTYTd-tHIATIGVDFKIKTVQIDGKNVKLQIWDTAGqERFRTITSSYYRGAQGII 85
gi 47209142   2 YLFKLLLIGDSGVGKSCLLLRFADGAYTd-sYISTIGVDFKIRTVDMDGKTVKLQIWDTAGqERFRTITSSYYRGAHGIV 80
gi 29841143   7 YLFKLLLIGDSGVGKSCLLIRFADESFSe-tYISTIGVDFKIRTIDLDGKVVKLQIWDTAGqERFRTITSSYYRGAQGII 85
gi 66825345  32 MLLKILVIGDSGVGKSCMLLRFADNRFTd-sYISTIGVDFCIRTIELDGKKIKLQIWDTAGqERFKTITTSYYRGAHGLI 110
gi 32492050   6 YLFKIIIIGDSGAGKSSLLLRFADDTYSe-sYMSTIGVDFKIKTVKIDNVTIKLQIWDTAGqERFRTITSTYYRGAHGII 84
gi 32398960  11 FLFKLVLIGDSGVGKSCLLLRFAQDDSFtdsYITTIGVDFRFRTIKIDDKIIKLQIWDTAGqERFRTITSAYYRGADGVV 90
gi 4585808   11 YLYKIILIGDSGVGKSCILLRFSDDHFTe-sYITTIGVDFRFRTIKVDDKIVKLQIWDTAGqERFRTITSAYYRGADGII 89
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                           ## #                          ###           
1UKV_Y       86 IVYDVTDQESFNGVKM-WLQEIDRYAtSTVLKLLVGNKCDLKDKRVVEYDVAKEFADANKMPFLETSALDSTNVEDAFLT 164
2FOL_A      103 VVYDVTDQESFNNVKQ-WLQEIDRYAsENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMT 181
gi 466170    86 IVYDITDMESFNNVKQ-WLDEIDRYAnDSVRKLLVGNKCDLAENRAVDTSVAQAYAQEVGIPFLETSAKESINVEEAFLA 164
gi 13537429  86 VVYSVIDLQTFQNVRQ-WLQEIERYAsETVIKLLIGNKCDLDDERAVTVEQGQELANSLNVSFMEASAKKSLNVDELFIR 164
gi 47209142  81 LVYDVTEQASFDNVRL-WMDEIERYAcEDVSRLLVGNKSDLLAQKVVDAAAAQDLASCLKIPFLETSAKNSENVEKVFLT 159
gi 29841143  86 IVYDVTDKTSFINVKS-WLQEIEHYAnSTVNRLLVGNKCDLPKSRAVDTVDAMNFAKEHQMPFLETSAKEAINVEDAFME 164
gi 66825345 111 IVYDITSMDSFNSIKR-WLIDVDRFAsPSVLKLIVGNKCDLNSKRAVDFKIAKKFADELNIPIMETSAKESTAIDEAFIK 189
gi 32492050  85 TVYDVTSRVSFESVKKtWLVDIEKYSsANISKLLIGNKVDLEDSRAVTYDEAREFAEQNNMDYIEASAKTAQNVEKAFES 164
gi 32398960  91 LVYDTTSTSSFDHIDE-WVTEVNRYT-TDSTKILIGNKCDLTSQKMVDFATGQKKAQELQVDFMESSAKNSTNVEECFVN 168
gi 4585808   90 IIYDTTDRNSFLHIND-WMNEINKYTnEDTCKLLVGNKADCKDDIEITTMEGQNKAKELNISFIETSAKDATNVELAFTM 168

                ....*...
Feature 1               
1UKV_Y      165 MARQIKES 172
2FOL_A      182 MAAEIKKR 189
gi 466170   165 MSAAIKKS 172
gi 13537429 165 IATDIMKN 172
gi 47209142 160 LASDIHRR 167
gi 29841143 165 MARQIKAS 172
gi 66825345 190 LASDIKKS 197
gi 32492050 165 IARALKDK 172
gi 32398960 169 IARKLLEK 176
gi 4585808  169 ITQELIKK 176

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