3QNK,5CK0,3JQ1


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 about 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: 400369
View PSSM: pfam07980
Aligned: 41 rows
Threshold Bit Score: 110.275
Threshold Setting Gi: 149931202
Created: 11-May-2020
Updated: 7-Aug-2020
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:
3QNK_B       236 KEIIFDVQYKSpDVYNNXXVCNXVTYINDKY----------------------GDRGWGGLGPTQELIDAFexadgtpat 293 Bacteroides fra...
CBK68230     277 SEVILAAQFSNdESTWGRYGNQMHLYYPAVYqgndigg---------ckrdisGGREFSYVSATEYTMQVF--------- 338 Bacteroides xyl...
Q8A056       261 NGSIFELNFDQ-SRNQSPDDDATASTYPSPSnvy-----------------pwTQSTVASLQFSNAMCKRLf-------- 314 Bacteroides the...
wustl:BV1736 299 KEAILVMPNRYgSDSGIRTRTMRNLVPWWNAtsistpd--------nklavdrFALTHASYDASMDYNRTFgrgvgvvrp 370 Bacteroides vul...
WP_013306461 287 TEGIM-MVIDReDYEGIGATSRGTSIQRQAVplwwr------------fintpDGQNGMTDSPSAEINQVTsvgrgigrn 353 Maribacter sp. ...
wustl:BV0492 276 MEAIWTFEMEYnRDVNGGTIDNPQQRRNWVPafhkldg--------mvnadsiGGRGNGRLRISNFVKYGL--------- 338 Bacteroides vul...
WP_005840243 287 KEALWKHRWFS-GNGSHGSSSGNYRLNRNDEyflcnvfnfgaitdtqefrlawEGGPNGLFMPTQHLLSLYvq------- 358 Bacteroides
wustl:BV0170 291 NEILMSCQHTS-SATGRFGNRTYSYFNPQFSnfsggwt---------qrgqyiGGMDFQRCRPTEYAYAIF--------- 351 Bacteroides vul...
Q8A5N7       264 SEVIWAIQYGLdKNYRGDGNPQQAQFGFNIValepdlf---------iknqndYSSVSRKYWVNPKAHELYt-------- 326 Bacteroides the...
Q5L7U9       283 NEIMFSVLAEE-GVGTGNKIPMGFAGEGKYG-------------------------ATGGSNLTSWLTLLYdipmwehny 336 Bacteroides fra...
3QNK_B       294 qysqa-----------------------padqvfdintcgiYEGREPRFYA-NIVFHGSQIF------------------ 331 Bacteroides fra...
CBK68230     339 -----------------------------------------DRVNDSRFWK-SFITCYGANEtksaptwtaedmpyapag 376 Bacteroides xyl...
Q8A056       315 -----------------------------------------DEQTDQWVTSnTVRGYGNTFV------------------ 335 Bacteroides the...
wustl:BV1736 371 tyf---------------------------aenslwylngnHDDGDLRHNS-KVGNWVHMEDlkynnp------------ 410 Bacteroides vul...
WP_013306461 354 rg-----------------------------thystkeiwkDANNDERHKLgNWLDMEDLVYnapsl------------- 391 Maribacter sp. ...
wustl:BV0492 339 -----------------------------------------YEKGDIRNSNyNIRRVMWYNKpgfskevgi--------- 368 Bacteroides vul...
WP_005840243 359 ----------------------------------------eDGTLDPRFHE-SFTTEWKANTaytwdkgtvnrfdresnv 397 Bacteroides
wustl:BV0170 352 -----------------------------------------DNVNDSRMWK-TFKTVYGLNNiaskaddvvatngitadq 389 Bacteroides vul...
Q8A5N7       327 -----------------------------------------DPEADTRYDA-TFKREYYINNpdnadygklgiyfpr--- 361 Bacteroides the...
Q5L7U9       337 sfkdvcmdygqvdrfnaespkpgttpydlqnlydrtgkytiTGDITRRMWS-SVKGWVTGPNsggapiglwvfepagrel 415 Bacteroides fra...
3QNK_B       332 ----------------------------------------------------FNADKGAVTVDRYLXDTPDKGDGSLTGY 359 Bacteroides fra...
CBK68230     377 vkegdkrfsggelgmkyivndpgdnryekypnapaytvlkdgkmcntytyvrYFKGQEHSWNVNEKTGNYYDIIPHKRSV 456 Bacteroides xyl...
Q8A056       336 -----------------------------------------------------------------LSSGTVIGNSNTEGY 350 Bacteroides the...
wustl:BV1736 411 ----------------------------------------------nsvyygKHLSYSCINDNGEEQILCNDTVRTWFDW 444 Bacteroides vul...
WP_013306461 392 -----------------------------------------------lesgnTYYGQNLELYLPDGTALCSDTIRNWYGW 424 Maribacter sp. ...
wustl:BV0492 369 -------------------------------------------dakgflvdkDKGIRNVTLKTGDQVIPHEGDSLNVFYP 405 Bacteroides vul...
WP_005840243 398 egkkievgqlaikfim--pqdenyaeesakklekdylvvdykdvyddakknvKMNYSYSNPSEGYTSDGKSENLFNFFYP 475 Bacteroides
wustl:BV0170 390 vptlgdqgiifilnkksdnrfkdatnsdygtvgrggiahsfvnpetnkwvpnVFPVYAGGQYVLNTYGVSGNPAQSNVFC 469 Bacteroides vul...
Q8A5N7       362 -------------------------------------wndksgmsnnakrfyPFKQDDEYVWYPQSTALPVLETASDRMP 404 Bacteroides the...
Q5L7U9       416 gpe----------------------------fyiepgkvndyteeqlkvmdvALESHERAWWKNETNGQNKPNLWNCNWW 467 Bacteroides fra...
3QNK_B       360 NVWKWIDydn-ynYPYAGAGSPDFSTNW-----IILRYAEIYLNDAEARLETGDVEG---ARKAVNXIRQRV-------- 422 Bacteroides fra...
CBK68230     457 ALSKFRD------GYRVSIASQFGTRDA-----IIARSADDVLMVAEAYIRKGEANYd-kAIEWMNKLRERAgykagedr 524 Bacteroides xyl...
Q8A056       351 LPFKFRIg----gKDGLSTTRSYKDANW-----ILYRMADVLLMKAEALIWKGGEANfaqALELINKIRTRA-------- 413 Bacteroides the...
wustl:BV1736 445 PHYKTWSespedeAPHLNNYQGSGYSDF-----YLYRLAETYLLRAEANYYLGNIEE---ATADVNIIRQRA-------- 508 Bacteroides vul...
WP_013306461 425 PQYKFFV------PDPKRVKPQGGHGDW-----YVYRIAETYLMRAEAHFWNDDNDL---AANDINAVRLRA-------- 482 Maribacter sp. ...
wustl:BV0492 406 HPTKWGA------YDETDDFGYAVVKDW-----PVMRLGETYLLRAEARFRQGNTQG---AADDINVLRDRAfkdyr--- 468 Bacteroides vul...
WP_005840243 476 SLNKHNSsny-yvANASKKRNGNLNATF------IMRTAEMYLIAAEADIYVNGGSN---ALKYINKIRTRA-------- 537 Bacteroides
wustl:BV0170 470 GINKTDD-------GSRTAEKGDAHRDV-----IMARTGETYLIKAEAQVRSGNFQD---AISTINQLRARAewkngedr 534 Bacteroides vul...
Q8A5N7       405 MVRKFSD-------TKIQWGEGGSREDV------IFRLGDTYLLCAEAYLGAGNKKL---ALERINSIRKRA-------- 460 Bacteroides the...
Q5L7U9       468 QLGKFRN-------LNPSELSSTFDINYggvdyPVLRLAEIYLLKAEAQIMQGHVSE---GVKTMNIIRDRAch------ 531 Bacteroides fra...
3QNK_B       423 ----------------------------------------------------------GLPDLTESD------------- 431 Bacteroides fra...
CBK68230     525 sknvdggqayknnpyc------------------sgkggghssegaiyweentyyesnNIEQETTAStkttmklnsvsdv 586 Bacteroides xyl...
Q8A056       414 ----------------------------------------------------------NVTTLSVQTna----------- 424 Bacteroides the...
wustl:BV1736 509 ----------------------------------------------------------KCDIFY---------------- 514 Bacteroides vul...
WP_013306461 483 ----------------------------------------------------------NADPITA--------------- 489 Maribacter sp. ...
wustl:BV0492 469 ------------------------------------------------------avapGAGKVTA--------------- 479 Bacteroides vul...
WP_005840243 538 ----------------------------------------------------------GANPLV---------------- 543 Bacteroides
wustl:BV0170 535 eyytdgsmaflksaggdednstalstlgkckdangtkinnteafkasflqkntyylstGIERTTDASslqissysslpae 614 Bacteroides vul...
Q8A5N7       461 ----------------------------------------------------------AKDATAYEAmk----------- 471 Bacteroides the...
Q5L7U9       532 --------------------------------------------------------qgSIKDMFVSQgdapytyqpg--- 552 Bacteroides fra...
3QNK_B       432 ------------------PEKLRELIRKERRIEFAFE-EQRFYDVRRw----KIGPETQTTLHGVRFVSPTEFKVTKTDI 488 Bacteroides fra...
CBK68230     587 ynstvdvpiynelgctsnADKMMCFLLNERTRELCGE-LQRWEDLAR-----TKTLDARWHKFNDGASRGLGEFKSEKHY 660 Bacteroides xyl...
Q8A056       425 ----------------vsQENMLGYLLQERDLEFAAE-GKRWYDLLR-----FGRSQNFKYKDQFINMIIENNSTVSASW 482 Bacteroides the...
wustl:BV1736 515 ------------------SKVNIDDIVDERARELYME-EWRFTELSRi----SYCLALSGKPDNEGKVYDVDKLYEDSFW 571 Bacteroides vul...
WP_013306461 490 ------------------SDVNIDYILDERARELYYE-ENRKTELTRi----AYIFAKTGRSAYNGQSYSLDNFSTKNFW 546 Maribacter sp. ...
wustl:BV0492 480 ------------------DQIDIDFILDERARELISE-ENRRMTLVR-----TNTLAERIKLNGDMEPAAPSNKVITGFD 535 Bacteroides vul...
WP_005840243 544 ------------------GVPTINTVLDERARELCGE-YARFYDLKR-----TGMLKDNSYLEEHHPDLAQFFKPEYA-- 597 Bacteroides
wustl:BV0170 615 -----deailsamgvngdKDRLINFILNERTRECLGE-WNRWEELSR-----TKTLVQRAKLFNPEAAANIADKHL---- 679 Bacteroides vul...
Q8A5N7       472 -----------------lTDLDINVIMDERARELMGE-HDRWFDLKR-----TQTLLTRVPAYNPFVVKYDNLNKNHL-- 526 Bacteroides the...
Q5L7U9       553 --------svmmiptnisPANALKELMYERLRELAAEdDCGWLDVARfpdvsMVDLADICRYRDPLQFFDPFGDPARGEY 624 Bacteroides fra...
3QNK_B       489 rtwn-----------------------drlyLTPVPHDEIVRS------------SVLKQNLGY 517 Bacteroides fragilis NCTC 9343
CBK68230     661 -------------------------------YRPIPQAFLDGItnsngsalsneeKKAMQNPGY 693 Bacteroides xylanisolvens XB1A
Q8A056       483 irsvlk--------------------ntdawYLPISQGEIDSN------------PNLIQNPYY 514 Bacteroides thetaiotaomicron
wustl:BV1736 572 whrinkynnyynkpdapivkgrkytigrhniNWPIPQSAIDANl----------lGKLGQNPGY 625 Bacteroides vulgatus ATCC 8482
WP_013306461 547 ydrimevtdfynlgi-rtihgdeytmspyhvLWPIPASAINANt----------qGTINQNVGY 599 Maribacter sp. HTCC2170
wustl:BV0492 536 ani--------------------------htLLPIPLTEIQLNk----------dGDLKQNPGY 563 Bacteroides vulgatus ATCC 8482
WP_005840243 598 -------------------------------LRPISTNFTSTLeg---------gGGYYQNPGY 621 Bacteroides
wustl:BV0170 680 -------------------------------LRPIPQTFLDQLqhedgtnlsdeeKAAMQNPGY 712 Bacteroides vulgatus ATCC 8482
Q8A5N7       527 -------------------------------VRPIPQDERNKV------------DGLSQNEGY 547 Bacteroides thetaiotaomicron
Q5L7U9       625 lwhlfne------------------ekvyrvLMPIPFTELSFF------------PEMKQNPGY 658 Bacteroides fragilis NCTC 9343
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