1D5C,1YZQ


Conserved Protein Domain Family
Rab6

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cd01861: Rab6 
Click on image for an interactive view with Cn3D
Rab GTPase family 6 (Rab6)
Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. 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: 206654
View PSSM: cd01861
Aligned: 33 rows
Threshold Bit Score: 209.786
Threshold Setting Gi: 56790168
Created: 6-Jan-2012
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 15 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:1D5C: Plasmodium falciparum Rab6 binds GDP and Mg2+, defined using 3.5 A contacts
    View structure with Cn3D
  • Comment:the Thr residue coordinates Mg2+

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               #######             # #                                                 
1D5C_A        2 YKLVFLGEQAVGKTSIITRFXYDTFDnnYQSTIGIDFLSKTLYLd-EGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVV 80
gi 56790168   7 KKVAFIGDATVGKTSLISRFMYDEFYdnYNVTVGTDFHSKIITInqKLRLRLQLLDIGSSMKHHSIVSSYVSNVNVCVLV 86
gi 67469385   7 HKVVFIGDCSVGKTCIIGRFTSKNFDmsYDATIGTDFVTQIMDVd-NKKIELQIWDTAGQERYRSLIPNYIRGASVVVIV 85
gi 62736246   5 CKVVFLGSAGVGKTSLLNRLMTDEFSnqYNTTIGVDFFTKPVQVq-GRTVTLQIWDTAGQERFKSLMPSYIRDSSVAVIV 83
gi 72536124   6 HKVVFVGNSAVGKTSIINQYMYDSVSadHQPTVGIDFFAKTVNYe-GKSIRMQIWDTAGQEKFHSLIPSYIRDSTVAIFV 84
gi 74834359   9 QKLVFLGNSFVGKTSIIERFVQNTFDpkSQPTVGIDFISKNMTId-GKTMRLLLWDTAGQERFHSLIPGYVRDAQCAVIV 87
gi 74833736  14 FKIVFIGNQAVGKTSIIARFVYEQIPeqHQPTIGIDFLSKCIQVd-NKTVRLQLWDTAGQERFRSLIPSYIRDSHAAVLC 92
gi 74834215  15 YKLVFLGDQSVGKTSIINRFMFDTFDgkDHPTVGIDFISKTLYYe-DRTIRLQLWDTAGQERFRSLIPSYIRDSAVAVVC 93
gi 72536122   6 HKVVLVGDSSVGKTSIINQFIYESISdeHQATVGIDFFSKQIEVd-GKVVKMQIWDTAGQEKFSSLIPSYIRDSTVAVFV 84
gi 62736244  10 HKIIFIGDSSVGKTSIINQYIYNSCTpqYNSTIGIDYLSKIVNEa-DKPIQLQIWDTAGQEKFHSLIPAYIRSSTIAVLV 88
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                         ## #                                ###       
1D5C_A       81 YDITNRQSFENTTKWIQDILNERGk-dVIIALVGNKTDLg------DLRKVTYEEGXQKAQEYnTXFHETSAK---AGHN 150
gi 56790168  87 YDITNQESFVSVQQWFKELQDITLtrtIQFYLVGNKIDLs------SQESVSIVQAKSFADSNnMKFICTSAL---SSMN 157
gi 67469385  86 YDISDKQTFNNIDHWFDEVPDRES---TLVYIVGNKVDSqrgvtkeEGMQKSYKWSARFIETSaLKDIGITDLfedIASN 162
gi 62736246  84 YDVSDEKSFDEAQEWYETVMHERGn-eAKCVLVGNKIDL-------ERRVDLKHVDDFAKPRQ-MQTIETSAK---TSSG 151
gi 72536124  85 FDITSRSSFEDLEKWFKMVLDIAN---PRLIIVGNKCDLd------AEREVTKDDAEKYAIIKsADYIETSAI---APTN 152
gi 74834359  88 FDVTSRHSFESLDRWFKEVKQTRGn-eALIVILGNKIDA-------ERVVSADEAREYAIKKD-ILYYEVSAK---TGKG 155
gi 74833736  93 YDVSNAQSFADIKAWLDYVREERGs-dVVGVLIANKIDI-------KDRVVTTQEGEKLAQEQdLLYYEVSAK---EGTN 161
gi 74834215  94 YDVEVKQSFDSVAKWIEDVRLERGn-dVIIFLVANKIDL-------ENRVVSTEQGAALAKEQdAHFIEVSAK---SGSN 162
gi 72536122  85 YDITSEESFDHLERWTKLVSDIAN---PSLVFVGNKTDLs------DARQVPIERLQNYSEEKkGKFIEVSAK---APTN 152
gi 62736244  89 YDITCKQSFDNIQTWYQMVINNAE---PAFIIVGNKSDLd------SERANSIEEGKKFANQInAKFIETSAI---TSEN 156
                       170
                ....*....|..
Feature 1                   
1D5C_A      151 IKVLFKKTASKL 162
gi 56790168 158 VSSLFSMISDGI 169
gi 67469385 163 LAPLAPKCTEAP 174
gi 62736246 152 VARLFKLISELA 163
gi 72536124 153 ITELFNLIASTP 164
gi 74834359 156 IEEAMEQICLAL 167
gi 74833736 162 VQQTFKNLALKL 173
gi 74834215 163 VELLFKQIAATL 174
gi 72536122 153 IKELFQMIAEIP 164
gi 62736244 157 ISQLFDIIIQIP 168

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