3QNK,5CJZ


Conserved Protein Domain Family
SusD_RagB

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pfam07980: SusD_RagB 
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SusD family
This domain is found in bacterial cell surface proteins such SusD and SusD-like proteins, as as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganisms that utilize a diverse array of glycans. Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain ###15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with##Bacteroides thetaiotaomicron##SusD (i.e alpha-helices and TPR regions). Based on this structural similarity, functional studies suggest that, RagB binding of glycans occurs at pockets on the molecular surface that are distinct from those of SusD.
Statistics
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PSSM-Id: 336890
View PSSM: pfam07980
Aligned: 59 rows
Threshold Bit Score: 107.566
Threshold Setting Gi: 500644436
Created: 26-Mar-2017
Updated: 23-May-2017
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       236 KEIIFd------VQYKS-PDVYNNXXVCNXVTY--INdkygdrg-----------------------wgglgpTQELIDA 283
gi 503071506 287 TEGIMm------VIDRE-DYEGIGATSRGTSIQrqAVplwwrfintp----------------dgqngmtdspSAEINQV 343
gi 156861184 285 PEVVMa------LAMEVgQVNTGWMRNMPFMPYncWDyfggtysq--------------------sgwncvclAPSWDNS 338
gi 500936988 290 KEVMLy------ADHTE-SSEYYNGGSLTYGSGgaPDnfagwmvtwnyts-----------irskngsasvssVQREANQ 351
gi 500648148 299 KEAILv------MPNRYgSDSGIRTRTMRNLVPwwNAtsistpdnklav------------drfalthasydaSMDYNRT 360
gi 500645087 276 MEAIWt------FEMEYnRDVNGGTIDNPQQRRnwVPafhkldgmvnad------------siggrgngrlriSNFVKYG 337
gi 500933182 258 KESLFtyqkdflLGPEDgLAGGGGSWLSSVFTHrtYElnaneliqdva--------------yggqalgwfypNNYLKSL 323
gi 491851820 273 DEIIWs------IQYTS-DLVYNGMDLTDIDANsmHRyfvgwynksaknpninidglwshsrvygreyrctmpTYYYISL 345
gi 500644436 291 NEILMs------CQHTS-SATGRFGNRTYSYFNpqFSnfsggwtqrgqy-------------iggmdfqrcrpTEYAYAI 350
gi 492426245 287 KEALWk------HRWFS-GNGSHGSSSGNYRLNrnDEyflcnvfnfgaitdtq----efrlaweggpnglfmpTQHLLSL 355
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       284 Fexadgtpatqysqa-padqvfdintcgiYEGREPRFY-A-NIVFHGS-QIFfna------------------------- 334
gi 503071506 344 Tsvgrgigrnrg-------thystkeiwkDANNDERHKlG-NWLDMEDlVYNapsl------------------------ 391
gi 156861184 339 GnvqpyggtdnpksfltdygdklgavyerFHDKDIRKQ-N-YVYNETT-GNYqgiflkgaikanygkg------------ 403
gi 500936988 352 Flgrpwtrmap--------pievftktfaDKTNDSRYD-G-TFAAVYR-GNWnlqgtglttvptltnangl--------- 411
gi 500648148 361 Fgrgvgvvrptyf-----aenslwylngnHDDGDLRHN-S-KVGNWVH-MEDlkynnp---------------------- 410
gi 500645087 338 L----------------------------YEKGDIRNS-NyNIRRVMW-YNKpgfskevgi------------------- 368
gi 500933182 324 Y----------------------------DQANDLRFK-TyYYSDNYQ-DYKi--------------------------- 346
gi 491851820 346 F-----------------------------DKFDKRRE-Q-TFQTAWC-RIPdnwnnepdysdtlli------------- 380
gi 500644436 351 F----------------------------DNVNDSRMW-K-TFKTVYG-LNNiaskaddvvatngitadqvptlgdqgii 399
gi 492426245 356 Yvq-------------------------eDGTLDPRFH-E-SFTTEWK-ANTaytwdkgtvnrfdresnvegkkievgql 407
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       335 --------------------------------------dkgAVTV-------DRYLXDTPDKGDGSLTGYNVWKWIDydn 369
gi 503071506 392 -------------------------------------lesgNTYYgqnlelyLPDGTALCSDTIRNWYGWPQYKFFVpd- 433
gi 156861184 404 -------------------------aalkadadrdgqdlvyVDQVgtflnlgRNLETVMSPRWGETNSGVRLVRYPVy-- 456
gi 500936988 412 ---------------------------------tikpgdavltflndepltpITYPSGQGDSGVGAGILPGRADYVIspn 458
gi 500648148 411 ------------------------------------nsvyyGKHLsyscindNGEEQILCNDTVRTWFDWPHYKTWSesp 454
gi 500645087 369 ---------------------------------dakgflvdKDKGirnvtlkTGDQVIPHEGDSLNVFYPHPTKWGAyd- 414
gi 500933182 347 -----------------------------------------NVPGnpkfgqpITNPAIAAPNGNYRAWHWSLKKYHDt-- 383
gi 491851820 381 --------------------------rtldvvsdeyvksyeDRGIivdnitdLYDINTGIPTINGRSCHHTMTKYLDps- 433
gi 500644436 400 filnkksdnrfkdatnsdygtvgrggiahsfvnpetnkwvpNVFPvyaggqyVLNTYGVSGNPAQSNVFCGINKTDDg-- 477
gi 492426245 408 aikfim--pqdenyaeesakklekdylvvdykdvyddakknVKMNysysnpsEGYTSDGKSENLFNFFYPSLNKHNSsny 485
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       370 y------------------nypyAGAGSPDFSTNWIILRYAEIYLNDAEARLETGDVEG--ARKAVNXIRQRV------- 422
gi 503071506 434 ----------------------pKRVKPQGGHGDWYVYRIAETYLMRAEAHFWNDDNDL--AANDINAVRLRA------- 482
gi 156861184 457 ----------------------pESAGIDFQNIDEVEFRLSEVVYTLAECKMRAGDTEG--AKELVYRVKTRY------- 505
gi 500936988 459 gisrivypgfwklgpyrtdnaggLGQPNAASTRPYPVAKFSELYLVAAEAAV-KGATGTlsARTLVNVIRARAgkwrw-- 535
gi 500648148 455 ed-----------------eaphLNNYQGSGYSDFYLYRLAETYLLRAEANYYLGNIEE--ATADVNIIRQRA------- 508
gi 500645087 415 ----------------------eTDDFGYAVVKDWPVMRLGETYLLRAEARFRQGNTQG--AADDINVLRDRAfkdyr-- 468
gi 500933182 384 ----------------------eKLPMTSNSYKDYMYYRLAETYLLASEAHHNLGNDTK--ALAYLNKVRRRGy------ 433
gi 491851820 434 ----------------------rDEAKREEGFKDLILMRLGEVYITLAEAYVRTNQPEK--AAEVITQLRKRA------- 482
gi 500644436 478 ----------------------sRTAEKGDAHRDVIMARTGETYLIKAEAQVRSGNFQD--AISTINQLRARAewknged 533
gi 492426245 486 y------------------vanaSKKRNGNLNATF-IMRTAEMYLIAAEADIYVNGGSN--ALKYINKIRTRA------- 537
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       423 -----------------------------------------------------------GLPDLTESDP----------- 432
gi 503071506 483 -----------------------------------------------------------NADPITAS------------- 490
gi 156861184 506 -----------------------------------------------------------FTDKSALEQPgpg-------- 518
gi 500936988 536 -------------------------------------------------------dnngNTAKIADNSAamtt------- 553
gi 500648148 509 -----------------------------------------------------------KCDIFYs-------------- 515
gi 500645087 469 -------------------------------------------------------avapGAGKVTAd------------- 480
gi 500933182 434 ----------------------------------------------------------tGNPESTVTTFdl--------- 446
gi 491851820 483 -----------------------------------------------------------LIDGHESALKvt--------- 494
gi 500644436 534 reyytdgsmaflksaggdednstalstlgkckdangtkinnteafkasflqkntyylstGIERTTDASSlqissysslpa 613
gi 492426245 538 -----------------------------------------------------------GANPLVg-------------- 544
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       433 ---------------EKLRELIRKERRIEFAFEEQR-FYDVRRwKIGPETQTTLHGVRFVSPTEFKVTKTDIrtwn---- 492
gi 503071506 491 ---------------DVNIDYILDERARELYYEENR-KTELTRiAYIFAKTGRSAYNGQSYSLDNFSTKNFWydrimevt 554
gi 156861184 519 -------------ftSFDMDWMLSEWGLEFLGEGRRrRTDLRRfDKFTQGQWWFFGRATDDGLSYPAKRDRKy------- 578
gi 500936988 554 -----------atpaIIDINYILAERSREFFGEGYR-WYDLVR-TQKWNEIAGKYSIGGSNYGQHTPEVVTRtida---- 616
gi 500648148 516 ---------------KVNIDDIVDERARELYMEEWR-FTELSRiSYCLALSGKPDNEGKVYDVDKLYEDSFWwhrinkyn 579
gi 500645087 481 ---------------QIDIDFILDERARELISEENR-RMTLVR-TNTLAERIKLNGDMEPAAPSNKVITGFDani----- 538
gi 500933182 447 --------------tAWTLNNYLDESARELAFENNR-WFLLKR-LGLLVERQNLYFRSSPSGTISGEVPLKMtpa----- 505
gi 491851820 495 -------------aaDVDMDFILEEGARELGCELNR-WYMLKR-SGKMVEWVKEHNPDITLIKDYHI------------- 546
gi 500644436 614 edeailsamgvngdkDRLINFILNERTRECLGEWNR-WEELSR-TKTLVQRAKLFNPEAAANIADKHL------------ 679
gi 492426245 545 ---------------VPTINTVLDERARELCGEYAR-FYDLKR-TGMLKDNSYLEEHHPDLAQFFKPEYA---------- 597
                        490       500       510       520       530       540
                 ....*....|....*....|....*....|....*....|....*....|....*....|
3QNK_A       493 -------------------drlyLTPVPHDEIVRS------------SVLK---Q-NLGY 517
gi 503071506 555 dfynlgi-rtihgdeytmspyhvLWPIPASAINANt----------qGTIN---Q-NVGY 599
gi 156861184 579 ----------------------eWYPLPQSALMVN------------PGLV---Q-NPNY 600
gi 500936988 617 --------------------hhyLRPIPQGQLDGMems------adeKAKY---Q-NPGY 646
gi 500648148 580 nyynkpdapivkgrkytigrhniNWPIPQSAIDANl----------lGKLG---Q-NPGY 625
gi 500645087 539 ---------------------htLLPIPLTEIQLNk----------dGDLK---Q-NPGY 563
gi 500933182 506 ---------------------mvNMPIPQSQIDLM------------GKPE---GfNVGY 529
gi 491851820 547 -----------------------YRPLPQDALYEV------------TNLDvfvQ-NKGY 570
gi 500644436 680 -----------------------LRPIPQTFLDQLqhedgtnlsdeeKAAM---Q-NPGY 712
gi 492426245 598 -----------------------LRPISTNFTSTLeg---------gGGYY---Q-NPGY 621
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