1KY2,1VG9,1YHN


Conserved Protein Domain Family
Rab7

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cd01862: Rab7 
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Rab GTPase family 7 (Rab7)
Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. 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: 206655
View PSSM: cd01862
Aligned: 31 rows
Threshold Bit Score: 286.098
Threshold Setting Gi: 67468620
Created: 6-Jan-2012
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 17 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:1KY2: Saccharomyces cerevisiae Ypt7p binds GppNHp, a GTP analog and Mg2+, defined using 3.5 A contacts
    View structure with Cn3D
  • Comment:the Thr residues coordinate Mg2+

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               #######         # #    #                          #                     
1KY2_A        9 LKVIILGDSGVGKTSLMHRYVNDKYSQQYKATIGADFLTKEVTVDgdkVATMQVWDTAGQERFQSLGVAFYRGADCCVLV 88
gi 17536699  10 LKVIILGDSGVGKTSLMNQYVNRRFSNQYKATIGADFLTRDVNIDd-rTVTLQIWDTAGQERFQSLGVAFYRGADCCVLA 88
gi 29841442   9 LKIIVIGDSGVGKTSLITQYIDKKFSNQYKATIGADFFTKQEVFDd-rLVTMQIWDTAGQERFQSLGVAFYRGADCCVLV 87
gi 13537439   8 LKVIILGDSGVGKTSLMNQFVNHKYSSVYKATIGADFLTKDLVVDn-hEVTMQIWDTAGNERFQSLGVAFYRGADCCALC 86
gi 60551617   9 LKLILIGNSGVGKSSFMTRFVDHRFTNLYRATIGVDFLTKEITVDr-rPVILQIWDTAGTERFHSLGSSLYRGAHCCLLV 87
gi 38649377   7 LKLLLIGNAGSGKSALMNQYVNCRFTNYYRATIGADFFTKELRVNd-kVVTVQIWDTAGTERFQSLGAALYRGTDCCLLV 85
gi 67470476  11 LKMILIGDSGVGKSSLMNQFIEKTFTAQYKATIGADFLTKEVTINg-tATTLQIWDTAGHEKFMSFGAAFYRGSDCCLLV 89
gi 67483055  11 FKIIILGDSGVGKTSLLNQYVTKQFSSQYKATIGADFMTKDITINd-qQISLQIWDTAGHERFASFGTAFYRGADVCMLV 89
gi 67468620   7 LKTILLGSSNVGKTALIHRFVNQKFTNSYKATIGADFMTKSIIVEg-kEVTMQTWDTAGNERFISLSIAFYRGADCCGLV 85
gi 74834804   8 LKIIILGDSGVGKTALVHQYVNKNFDNRYKATIGADFLTRDVEIDg-kLVTLQIWDTAGQERFQSLGSAFYRGADACVLV 86
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                            ## #                                       
1KY2_A       89 YDVTNASSFENIKSWRDEFLVHAnvnspeTFPFVILGNKIDAeeskKIVSEKSAQELAKSLg------------------ 150
gi 17536699  89 FDVTNAASFKSLDSWRDEFLIQAsprdpdHFPFVLLGNKVDLes-qRAVSSKRAQSWCQTKg------------------ 149
gi 29841442  88 YDVSMTSTFKTLDSWRNEFLVQSsprnpeKFPFIVIGNKCDLd--nRAISENRARQWCQANg------------------ 147
gi 13537439  87 YDVNDPKTFESLNNWREEFLVQAspknqdQFPFVVLGNKVDTyegsPDAIKKKAEQWCSEHf------------------ 148
gi 60551617  88 FDVTSSVSFEALDVWKKEFLVQAcpsdpaAFPFIVLGNKIDLd--hRQVSTSKAQKWCVDIg------------------ 147
gi 38649377  86 FDVTSPNSFHALDNWHREFLVQAdpvspgSFPFVVIGNKTDLe--eRQVSLREAEEWCKTYn------------------ 145
gi 67470476  90 LDVTNEASFKSLDTWKKEFLNGAnvtnpnDFPFVVLVNKMDEdpskHVVSVSDVKQWCENNg------------------ 151
gi 67483055  90 CDVTVAESFEHLEVWRKEFISGGnpsdpeSFPYVVIANKNDCepanRAVSSDQLRQWCVTNg------------------ 151
gi 67468620  86 FDVSNPKSFEQLTMWKNEFLKNCttnkngKFPFVIIGNKIDKg---SVISKEAVDDWIQFNdl----------------- 145
gi 74834804  87 FDLTDSESFSHINSWLEEFRAQAg-----QRECVLIGNKSDLte-rRQVTSRTAEAWCESLkngeggdaslgaaageetm 160
                       170       180       190
                ....*....|....*....|....*....|...
Feature 1               ###                      
1KY2_A      151 -dIPLFLTSAKNAINVDTAFEEIARSALQQNQA 182
gi 17536699 150 -nIPYYEVSAKEALNVEAAFLAIARDALARESQ 181
gi 29841442 148 -nLPYFECSAKENTNVELAFEHIIRVAIDEESA 179
gi 13537439 149 -nIPFFETSAKNATNVDAAFQSIAQAAIAQKGT 180
gi 60551617 148 --AEYFESSAKEDIGVDKTFHSAARAALQYLKS 178
gi 38649377 146 --AKYFETSAKESRNVDEAFLEAIKLAFNNHQE 176
gi 67470476 152 -nIPLYETSAKTGAQVDTAFLDVATKVVQSMKE 183
gi 67483055 152 --YEFFECSAKTGWNVDSAFTKAATLVAMRQKE 182
gi 67468620 146 -dAIYVESSALTGDNVDFVFECLAKKALESEPL 177
gi 74834804 161 gsIQYFEASAKANVGVEEAFLTVSKAALAKKAT 193

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