5CJZ,3JQ1


Conserved Protein Domain Family
SusD_RagB
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pfam07980: SusD_RagB (This model is not part of the current CDD release)
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.
Links
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Statistics
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PSSM-Id: 518007
Aligned: 34 rows
Threshold Bit Score: 123.775
Created: 14-Feb-2025
Updated: 28-Apr-2025
Structure
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Program:
Drawing:
Aligned Rows:
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PubMed ReferencesClick to see Conserved Features Help
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
5CJZ_A        324 EIIW-------GLSNQFDFYSRYPLRILKKsdgtwha------------------gysgvsPTLYTFEHFYTANGKLP-E 377 Bacteroides th...
Q8A5N7        265 EVIWaiqygldKNYRGDGNPQQAQFGFNIValepdlfiknq---------ndyssvsrkywVNPKAHELY---------- 325 Bacteroides th...
12_pfamImport   2 EALWkhr-wfsGNGSHGSSSGNYRLNRNDEyflcnvfnfgaitdtqefrlaweggpnglfmPTQHLLSLY---------- 70 
2_pfamImport    2 EILMscq-htsSATGRFGNRTYSYFNPQFSnfsggwtqrgq---------yiggmdfqrcrPTEYAYAIF---------- 61 
10_pfamImport   2 EAILvmpnrygSDSGIRTRTMRNLVPWWNAtsistpdnklav--------drfalthasydASMDYNRTFGRGVGVVRpT 73 
WP_013306461  288 EGIMmvi-dreDYEGIGATSRGTSIQRQAVplwwrfintp------------dgqngmtdsPSAEINQVTSVGRGIG--R 352 Maribacter sp....
4_pfamImport    2 EAIWtfemeynRDVNGGTIDNPQQRRNWVPafhkldgmvnad--------siggrgngrlrISNFVKYGL---------- 63 
Q8A353        269 EHIFsvp-ffrDKDALADQSLGSNIAHLFNpagvqvggklvs-------gnpygkgagahrVQKWFIKYFQDDQGNLG-Y 339 Bacteroides th...
8_pfamImport    2 DPIFeip-fakESTGNTGYSQGPTSTVNEGktlgknvw---------------geskgdirLSAFYRYSF---------- 55 
Q8A2H4        283 ESIWeaefagnNTSDTQAEGRIGNIIGLAGpdlssksdvtga--------kdpgygyafiySTPKLYNLY---------- 344 Bacteroides th...

5CJZ_A        378 KDldftpssewfesaGISSREDIIKLNVGREPRFYA-WMAFDGGDYGTkf------------------------------ 426 Bacteroides th...
Q8A5N7        326 -------------------------TDPEADTRYDA-TFKREYYINNPdnadygklgiyfpr------------------ 361 Bacteroides th...
12_pfamImport  71 -----------------------VQEDGTLDPRFHE-SFTTEWKANTAytwdkgtvnrfdresnvegkkievgqlaikfi 126
2_pfamImport   62 --------------------------DNVNDSRMWK-TFKTVYGLNNIaskaddvvatngitadqvptlgdqgiifilnk 114
10_pfamImport  74 YF-------------AENSLWYLNGNHDDGDLRHNS-KVGNWVHMEDLkynnp--------------------------- 112
WP_013306461  353 NR-------------GTHYSTKEIWKDANNDERHKLgNWLDMEDLVYNapsl---------------------------- 391 Maribacter sp....
4_pfamImport   64 --------------------------YEKGDIRNSNyNIRRVMWYNKPgfskevgi------------------------ 93 
Q8A353        340 SD-------------PSVDASIDESKLISKDYRIEV-TFWRRFQQKN--------------------------------- 372 Bacteroides th...
8_pfamImport   56 ---------------------------DENDKRRDFiNGLWYYGNSA--------------------------------- 75 
Q8A2H4        345 --------------------------VNNGDTKRFNwSIAPFEYKEAGgkntgvthr----------------------- 375 Bacteroides th...

5CJZ_A        427 ---------------------------------aaGSPLKLEMRNSEMHGYNPSLFNRDHSVTGFLTQKFVDp-----vT 468 Bacteroides th...
Q8A5N7        362 ----------------------wndksgmsnnakrFYPFKQDDEYVWYPQSTALPVLETASDRMPMVRKFSD-------T 412 Bacteroides th...
12_pfamImport 127 m--pqdenyaeesakklekdylvvdykdvyddakkNVKMNYSYSNPSEGYTSDGKSENLFNFFYPSLNKHNSsny-yvaN 203
2_pfamImport  115 ksdnrfkdatnsdygtvgrggiahsfvnpetnkwvPNVFPVYAGGQYVLNTYGVSGNPAQSNVFCGINKTDD-------G 187
10_pfamImport 113 -------------------------------nsvyYGKHLSYSCINDNGEEQILCNDTVRTWFDWPHYKTWSespedeaP 161
WP_013306461  392 --------------------------------lesGNTYYGQNLELYLPDGTALCSDTIRNWYGWPQYKFFVp------D 433 Maribacter sp....
4_pfamImport   94 ----------------------------dakgflvDKDKGIRNVTLKTGDQVIPHEGDSLNVFYPHPTKWGAy------D 139
Q8A353        373 ----------------------------------------NNTGVLGNIVTVYPAAGGNSQENWGYIRKFID-------- 404 Bacteroides th...
8_pfamImport   76 -------------------------------------------------NNATQDSCMIRADYTVHNNKWSKlwa-nagQ 105
Q8A2H4        376 ---------------------------efeqgklaEVMSQYGQQRGTYQYADDTEKTTATKNFSRMCGKYRRe-----yE 423 Bacteroides th...

5CJZ_A        469 EfytAGGSTSGTSAPTILFRLAELYLNVAECHAALGNTQE--AIDALNPVRERA-------------------------- 520 Bacteroides th...
Q8A5N7        413 K---IQWGEGGSREDV-IFRLGDTYLLCAEAYLGAGNKKL--ALERINSIRKRA-------------------------- 460 Bacteroides th...
12_pfamImport 204 A---SKKRNGNLNATF-IMRTAEMYLIAAEADIYVNGGSN--ALKYINKIRTRA-------------------------- 251
2_pfamImport  188 S---RTAEKGDAHRDVIMARTGETYLIKAEAQVRSGNFQD--AISTINQLRARAewkngedreyytdgsmaflksaggde 262
10_pfamImport 162 H---LNNYQGSGYSDFYLYRLAETYLLRAEANYYLGNIEE--ATADVNIIRQRA-------------------------- 210
WP_013306461  434 P---KRVKPQGGHGDWYVYRIAETYLMRAEAHFWNDDNDL--AANDINAVRLRA-------------------------- 482 Maribacter sp....
4_pfamImport  140 E---TDDFGYAVVKDWPVMRLGETYLLRAEARFRQGNTQG--AADDINVLRDRAfkdyr--------------------- 193
Q8A353        405 P---QGINNRTNENDMPRLRLSDMYLIRAEALNELGKYTE--ACQAIDMVRERA-------------------------- 453 Bacteroides th...
8_pfamImport  106 F---TNLSASNTGINFPYMRYTDVLLMNAEAVNELEGPTAt-AQESLRQVHARA-------------------------- 155
Q8A2H4        424 A---DKKDKNYTSINFPILRYADVLLMIAEAENEANNGPTtlAYQCMKEVRERA-------------------------- 474 Bacteroides th...

5CJZ_A        521 ----------------------------------------GIPKLTLAdi-----------------------tnNMTIK 537 Bacteroides th...
Q8A5N7        461 ----------------------------------------AKDATAYEam-----------------------klTDLDI 477 Bacteroides th...
12_pfamImport 252 ----------------------------------------GANPLV-----------------------------GVPTI 262
2_pfamImport  263 dnstalstlgkckdangtkinnteafkasflqkntyylstGIERTTDAsslqissysslpaedeailsamgvngdKDRLI 342
10_pfamImport 211 ----------------------------------------KCDIFY-----------------------------SKVNI 221
WP_013306461  483 ----------------------------------------NADPITA----------------------------SDVNI 494 Maribacter sp....
4_pfamImport  194 ------------------------------------avapGAGKVTA----------------------------DQIDI 209
Q8A353        454 ----------------------------------------RKANGTERaypkyigsdr--------pdnigrtltKQEFR 485 Bacteroides th...
8_pfamImport  156 ----------------------------------------FDDQSVVSayiaq------------------vassKETFL 177
Q8A2H4        475 ----------------------------------------GLNELPDMt--------------------------QEEFR 488 Bacteroides th...

5CJZ_A        538 DWVHNERFVELWNEGHRFFDVRRW-------------------------------------------------------- 561 Bacteroides th...
Q8A5N7        478 NVIMDERARELMGEHDRWFDLKR--------------------------------------------------------- 500 Bacteroides th...
12_pfamImport 263 NTVLDERARELCGEYARFYDLKR--------------------------------------------------------- 285
2_pfamImport  343 NFILNERTRECLGEWNRWEELSR--------------------------------------------------------- 365
10_pfamImport 222 DDIVDERARELYMEEWRFTELSRI-------------------------------------------------------- 245
WP_013306461  495 DYILDERARELYYEENRKTELTRI-------------------------------------------------------- 518 Maribacter sp....
4_pfamImport  210 DFILDERARELISEENRRMTLVR--------------------------------------------------------- 232
Q8A353        486 WLVFMERGLEFAGEQKRWFDLIR--------------------------------------------------------- 508 Bacteroides th...
8_pfamImport  178 KAVLDERKWEFAGENMRWRDLVRNnlygqeivysflrylsvgmsnagsstgfeddiaehdgsaylddlpesmyyhvlpqt 257
Q8A2H4        489 QTVKDERAMELCFEYTRRFDLIRW-------------------------------------------------------- 512 Bacteroides th...

5CJZ_A        562 -------------------------AEGAKYFGANKREGLNAEVQSPTFEEFNKRTTVDAPYVWENr------------- 603 Bacteroides th...
Q8A5N7        501 -------------------------TQTLLTRVPAYNPFVVKYDNLNKNHL----------------------------- 526 Bacteroides th...
12_pfamImport 286 -------------------------TGMLKDNSYLEEHHPDLAQFFKPEYA----------------------------- 311
2_pfamImport  366 -------------------------TKTLVQRAKLFNPEAAANIADKHL------------------------------- 389
10_pfamImport 246 -------------------------SYCLALSGKPDNEGKVYDVDKLYEDSFWWHRINKYNNYYNKpdapivkgr----- 295
WP_013306461  519 -------------------------AYIFAKTGRSAYNGQSYSLDNFSTKNFWYDRIMEVTDFYNLgirtihgd------ 567 Maribacter sp....
4_pfamImport  233 -------------------------TNTLAERIKLNGDMEPAAPSNKVITGFDANIHT---------------------- 265
Q8A353        509 -------------------------MKYDENTQMYDYIKDTFIPSRPAADVQKQGVMAARKK------------------ 545 Bacteroides th...
8_pfamImport  258 vewrvdvnqvygypypnkildmlyiYNPYKSANQPATALVAVDGATWKMAEFYQWSNDSEPTNQCKysfygyirhteqgm 337
Q8A2H4        513 -------------------------GEYVKNMRALVTEAQSGNNWTQGPTNVYTYFNISSTYN----------------- 550 Bacteroides th...

5CJZ_A        604 --------------------------mYLNPVFYNEVYKN------------PQMVQ-A-PGY 626 Bacteroides thetaiotaomicron VP...
Q8A5N7        527 ----------------------------VRPIPQDERNKV------------DGLSQ-N-EGY 547 Bacteroides thetaiotaomicron
12_pfamImport 312 ----------------------------LRPISTNFTSTLeg---------gGGYYQ-N-PGY 335
2_pfamImport  390 ----------------------------LRPIPQTFLDQLqhedgtnlsdeeKAAMQ-N-PGY 422
10_pfamImport 296 -------------------kytigrhnINWPIPQSAIDANl----------lGKLGQ-N-PGY 327
WP_013306461  568 -------------------eytmspyhVLWPIPASAINANt----------qGTINQ-N-VGY 599 Maribacter sp. HTCC2170
4_pfamImport  266 ----------------------------LLPIPLTEIQLNk----------dGDLKQ-N-PGY 288
Q8A353        546 ----------------------------YFPIPFAEVSRN------------DGVQQ-N-PGY 566 Bacteroides thetaiotaomicron
8_pfamImport  338 ivlvkdgtespldgnsvpevndlppvrYILPYPNAAIQRS------------AGVYK-NyYGY 387
Q8A2H4        551 ----------------------------YFPIPDAEMSVN------------KDITQnN-PGW 572 Bacteroides thetaiotaomicron
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