1M8W,3BX3


Conserved Protein Domain Family
Pumilio

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cd07920: Pumilio 
Click on image for an interactive view with Cn3D
Pumilio-family RNA binding domain
Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.
Statistics
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PSSM-Id: 153420
View PSSM: cd07920
Aligned: 45 rows
Threshold Bit Score: 286.41
Threshold Setting Gi: 17534639
Created: 30-Sep-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA binding
Conserved site includes 28 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Structure:1M8W: human Pumilio1 binds a high-affinity RNA ligand, contacts at 4A
    View structure with Cn3D
  • Comment:Each of the protein's repeats contacts a different RNA base, utilizing three conserved residues per repeat that determine sequence specificity
  • Structure:3BX3: Saccharomyces cerevisiae Puf4p binds the 3' UTR recognition sequence of COX17 RNA, contacts at 4A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
1M8W_A     16 NLQLREIA--------GHIMEFSQDq-HGSRFIQLKLEra--------tPAERQLVFNe----iLQAAYQLMVDv----f 70   human
Q09829    457 IPHLVGFL--------GHLSTICKDq-YGCRYLQKLLDen--------pKVNASLFFPe----iRQSVVQLMIDp----f 511  fission yeast
AAQ84132  190 NITPEGLR--------GSVYEIAKDq-HGCRFLQRLLGgs-------ngDGEFVRIIMne---vVPHVAELMTDq----y 246  Trypanosoma cruzi
P39016    199 SSSMVEISalp--lrdLDYIKLATDq-FGCRFLQKKLEt----------PSESNMVRDlmyeqiKPFFLDLILDp----f 261  baker's yeast
EEQ41907  277 KLPLTQLK--------SEILKLAKDq-YGCRFLQKKIDeslvp-nyqvrLANFEIIFNq----iYSHVYELIVDp----f 338  Candida albicans ...
EES98380  310 APQPDPLAge-----hERKLVLSFKesTGCKALQQYMVdfp-----dksHYLLDVFIT------EYGTPSLMEGllihpa 373  Giardia intestina...
NP_199123 203 ASSMENGR--------GSYFSIATDr-VWSKELEKTIFvg--------tKETIDMIFDg----lIVGICELMVDp----f 257  thale cress
CAN67257  180 SAQIQSMQp-------CQIIEMALNf-SGSFLLRSALAek--------kPESKSTIFEg----lIAHIVTLAVHp----s 235  wine grape
NP_192596 137 FVSLDDDAygymygirNTLLSRAKDg-IESHMLQYVIAkg--------lKETIDKIFDn----lISHVCELMLDy----y 199  thale cress
EER11076  366 SVTLEEIQ--------DKILEMAMDr-SGSRVLQKLISdtsasaadggaHDELEKLIDaii-heIQPVLSRIMCdt---y 432  Perkinsus marinus...
Feature 1      ##  #                                  ##  #                                   
1M8W_A     71 GNYVIQKFFEFgsLEQKLALAERir---gHVLSLALQmYGCRVIQKALEFIp---sDQQNEMVRELd------GHVLKCV 138  human
Q09829    512 GNYMCQKLFVYasREQKLSMLNGig---eGIVDICSNlYGTRSMQNIIDKLts--nEQISLLLKIIi------PSLTTLA 580  fission yeast
AAQ84132  247 ANFLIQKLFDMmpQDVRYKVARVaa---pKIISIALTpHGTFSVQKMVETIas--rEEMDILREALs------KDVVRLV 315  Trypanosoma cruzi
P39016    262 GNYLVQKLCDYltAEQKTLLIQTiy---pNVFQISINqYGTRSLQKIIDTVdn--eVQIDLIIKGFsqeftsiEQVVTLI 336  baker's yeast
EEQ41907  339 GNYLIQKLIVYc-NESNLDLLMEil--qyNLFQISINqHGTRALQKIIDSLnn--sHQLGLLIKGLk------PYIIELI 407  Candida albicans ...
EES98380  374 GNYCFQKIIEGsdATQRLRILLLiq---dSLFDICHNlHGTRSIQKLLERVsl--dEEKAIFAQQLgt----gDRIIKLI 444  Giardia intestina...
NP_199123 258 GNDVVKLLIGKcsSEQIILIVDVvtrhisKFVNICFNpIGTLAIQVLLTSIheranNQIPRIMDAIs------SVALQLT 331  thale cress
CAN67257  236 GCNVFIRLTEAcdANQLSQILSKlilppsTIIRVSHDpIGSKSIQRLIQVLrr--sPLVVPVVTALa------AGFYELM 307  wine grape
NP_192596 200 GHKVFRKLMEKctDEQITRVLDIvleepfEFVRLCVHtHGTHAIQGLMRSLcs--eEQISRFMETL-------CYVSLLL 270  thale cress
EER11076  433 ANYMCQQLFQVssASQRIALLRNvl---eNIVYISQDrRGTHSLQALIACMqt--pQEHALLAETLh------GNVNKMA 501  Perkinsus marinus...
Feature 1            #  #                                             ##  #                   
1M8W_A    139 Kd-qNGNHVVQKCIECv------------qPQSLQFIIDAFkg--qVFALSTHpYGCRVIQRILEHCl----pDQTLPIL 199  human
Q09829    581 Cd-nNGTHVLQKCIAKf------------pPEKLEPLFLSMee--nLITLATNrHGCCILQRCLDRTn----gDIQERLV 641  fission yeast
AAQ84132  316 Kd-aHGNHVIQKVLQRf------------sHADKEFIYAAVgs--dCISIAKNkQGCCVLQRCLEYAs----cSQRATLV 376  Trypanosoma cruzi
P39016    337 Nd-lNGNHVIQKCIFKf------------sPSKFGFIIDAIveqnnIITISTHkHGCCVLQKLLSVCt----lQQIFKIS 399  baker's yeast
EEQ41907  408 Kd-lNGNHVIQKILNKy------------ePPDCQFIYDSIid--dLYIVATHkHGCCVLQKCLNHVt----lQQLGEFS 468  Candida albicans ...
EES98380  445 Md-iNGNHCVQRCIEAf------------sPKDCAFIYSQIvr--eLVLVSTHqHGCCIIQRCLDLCs----eAQRVQIV 505  Giardia intestina...
NP_199123 332 Rn-tNAKYVILACFRMf------------tSSQCRRLLEVVsq--hCYQIAIDqNGCCLLQQCFDKErvp-nhEIRQRLI 395  thale cress
CAN67257  308 Kd-qQGAMVISRCLALl------------sSEQNEELYRAAil--pCVALATHaKGCIALNSFINNVi----gPYRDLLL 368  wine grape
NP_192596 271 TkdvIAHRVILFCFNQf------------sPSHTRYLLEVIvq--nCYQVAIDqNGCCMLKKLIRQSs----rELRDPLI 332  thale cress
EER11076  502 Ld-vHATHVLQQTITKctpdgpgkeyshlpMADFGFIFDDIyr--nLEALAGDpNGLGVVKKCISHApwyddgSYVEKYK 578  Perkinsus marinus...
Feature 1                            ## ##  #                                    ## ##  #     
1M8W_A    200 EELHQHTe--------QLVQd--QYGNYVIQHVLEHGr-----PEDKSKIVAEIr---gNVLVLSQHKFASNVVEKCVTH 261  human
Q09829    642 NSIIKSCl--------LLVQn--AYGNYLVQHVLELNi-----QPYTERIIEKFf---gNICKLSLQKFSSNAIEQCIRT 703  fission yeast
AAQ84132  377 NQILRCCl--------QIAEd--PFGNYVLQYVLESNd-----SKTTDTIAIAFl---pHLVQLCMNKFSSNVIEKVLRG 438  Trypanosoma cruzi
P39016    400 VKIVQFLp--------GLINd--QFGNYIIQFLLDIK------ELDFYLLAELFnrlsnELCQLSCLKFSSNVVEKFIKK 463  baker's yeast
EEQ41907  469 RAILKFEnf------kLLINd--QFGNYVLQYLISINs-----LDINFQIFQNFvn--fGISNLCNLKFSSNVVEKFLKN 533  Candida albicans ...
EES98380  506 TAIKDHVm--------ELIVd--RFGNYVFQYSLEKAsnglcgPITTDDLIRPVl---gQEAFLVNQKFSSHAIEKCLKY 572  Giardia intestina...
NP_199123 396 SEVIEHAl--------KLCLn--CHGNYVVQYVVELDn-----QHETDLLVNKLl---rNYAHLARNKYGSHVVQKLLKL 457  thale cress
CAN67257  369 HKITDNTv--------FLSQd--PRGNFVVQHILELHh-----PVFTSKICHLLq---gYYVRLSVQKSGSHIVEKCLKS 430  wine grape
NP_192596 333 KEIISIAvrlcgncygTLTPkslLVRNYVVQYLLRLKd-----YEVTSALSKHLd---gNYVQLSYDKYGSHVVQKCLES 404  thale cress
EER11076  579 SKMLNKLq--------YFVEn--PYANYAVQHALEIWg-----PEVCTDIITKIs---eSIISMAIHKFASNVVETALKV 640  Perkinsus marinus...
Feature 1                                                                       ## ##  #      
1M8W_A    262 asr---------teRAVLIDEVCTMndg---------------------------phsALYTMMKDQYANYVVQKMIDVA 305  human
Q09829    704 asp---------stREQMLQEFLSFp--------------------------------NIEQLLDDCYANYVMQRFLNVA 742  fission yeast
AAQ84132  439 asq---------pvQEMYVETMCSPd--------------------------------VVSRLIQDDFGNYVLQTALTIC 477  Trypanosoma cruzi
P39016    464 --------------LFRIITGFIVNnnggasqrtavasddvinasmnillttidiftvNLNVLIRDNFGNYALQTLLDVK 529  baker's yeast
EEQ41907  534 cyanesvnvsfsnlKFELIYIILVS---------------------------------DLNVLINDPYGNYVIQTMIDIM 580  Candida albicans ...
EES98380  573 gsk---------kmRALITENVMASg--------------------------------SFLSLAMDKFGNYVIQKAFCDA 611  Giardia intestina...
NP_199123 458 rg-----------iDSKLIVVDLLR---------------------------------GIDTLLLDPFGNYVIQTAWFVS 493  thale cress
CAN67257  431 h------------wMSFAVKELTTSg--------------------------------RLPQLAHDQFGNYVIQTALRVT 466  wine grape
NP_192596 405 --------------REFSSRRIIAEll------------------------------sDIDSLLVDPYGDYVIQTAWIVS 440  thale cress
EER11076  641 spd---------dmRVMLIHRLIDYgnts-------------------------cqnaAMITLMNSAYGVFVMSTALRLA 686  Perkinsus marinus...
Feature 1                                                            #  #     
1M8W_A    306 e---------------------------pGQRKIVMHKIRPHIAtlr-----kytYGKHILAKL 337  human
Q09829    743 d---------------------------eSQKFLILRSISHVIPkiq-----ntrHGRHILAKL 774  fission yeast
AAQ84132  478 s---------------------------sAQAESLVSAVRPLMPiir-----napYAKKLEGKI 509  Trypanosoma cruzi
P39016    530 nys------------------------plLAYNKNSNAIGQNSSstlnygnfcndFSLKIGNLI 569  baker's yeast
EEQ41907  581 vnpqvnyqnnnidklslvlpdrqdngvfqSQQELQIAIIEYWFQncki----vssFGKRIQSKI 640  Candida albicans WO-1
EES98380  612 t----------------------------DEQKKIISQRVLASPevm-----scsYSRHLVQMC 642  Giardia intestinalis ATCC 50581
NP_199123 494 k---------------------------eDVRQMLRYYIERNIRlmr-----cnkFGNKILEKL 525  thale cress
CAN67257  467 kda------------------------niQLYRSLLEALEPYLPsla-----shlHGKNLFRLI 501  wine grape
NP_192596 441 -----------------------------EVRDKHDDSESFYVD-----------FYQLILWLV 464  thale cress
EER11076  687 pt--------------------------tELCEQIYGALVRNYQrlpds-rnkqkWDKVLVMAE 723  Perkinsus marinus ATCC 50983

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