NCBI CDD Logo
?
cd11340: AmyAc_bac_CMD_like_3 
Click on image for an interactive view with Cn3D
Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
Links
?
Statistics
?
PSSM-Id: 200479
View PSSM: cd11340
Aligned: 35 rows
Threshold Bit Score: 611.138
Threshold Setting Gi: 299139735
Created: 19-Jul-2011
Updated: 17-Jan-2013
Structure
?
Program:
Drawing:
Aligned Rows:
Hierarchy
?
Display:
 
Conserved site includes 14 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:3EDF: Flavobacterium Sp. 92 binds cellohexaose, contacts at 4A
    View structure with Cn3D
  • Structure:3EDF: Flavobacterium Sp. 92 binds alpha-cyclodextrin, contacts at 4A
    View structure with Cn3D

cd11340 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd11340 is a member of the superfamily cl07893.
cd00551:AmyAc_familycd11313:AmyAc_arch_bac_AmyAcd11314:AmyAc_arch_bac_plant_AmyAcd11315:AmyAc_bac1_AmyAcd11316:AmyAc_bac2_AmyAcd11317:AmyAc_bac_euk_AmyAcd11318:AmyAc_bac_fung_AmyAcd11319:AmyAc_euk_AmyAcd11320:AmyAc_AmyMalt_CGTase_likecd11321:AmyAc_bac_euk_BEcd11322:AmyAc_Glg_BEcd11323:AmyAc_AGScd11324:AmyAc_Amylosucrasecd11325:AmyAc_GTHasecd11326:AmyAc_Glg_debranchcd11327:AmyAc_Glg_debranch_2cd11328:AmyAc_maltasecd11329:AmyAc_maltase-likecd11330:AmyAc_OligoGlucd11331:AmyAc_OligoGlu_likecd11332:AmyAc_OligoGlu_TScd11333:AmyAc_SI_OligoGlu_DGasecd11334:AmyAc_TreScd11335:AmyAc_MTase_Ncd11336:AmyAc_MTSasecd11337:AmyAc_CMD_likecd11338:AmyAc_CMDcd11339:AmyAc_bac_CMD_like_2cd11340:AmyAc_bac_CMD_like_3cd11341:AmyAc_Pullulanase_LD-likecd11343:AmyAc_Sucrose_phosphorylase-likecd11344:AmyAc_GlgE_likecd11345:AmyAc_SLC3A2cd11346:AmyAc_plant_IsoAcd11347:AmyAc_1cd11348:AmyAc_2cd11349:AmyAc_3cd11350:AmyAc_4cd11352:AmyAc_5cd11353:AmyAc_euk_bac_CMD_likecd11354:AmyAc_bac_CMD_likecd11355:AmyAc_Sucrose_phosphorylasecd11356:AmyAc_Sucrose_phosphorylase-like_1cd11359:AmyAc_SLC3A19496853022587409029913973534758850925642406931288669633266753928403776583816389254444955293491121500101202245405273011640793013122292245365702555346953399032713132038073343648861H3G A3EDD A3EDF A255535256119469265333892986119774796912147162600616483326681093298944301240090123121309961923591723199540539496853022587409029913973534758850925642406931288669633266753928403776583816389254444955293491121500101202245405273011640793013122292245365702555346953399032713132038073343648861H3G A3EDD A3EDF A25553525611946926533389298611977479691214716260061648332668109329894430124009012312130996192359172319954053
cd11340 Sequence Cluster
cd11340 Sequence Cluster
Sub-family Hierarchy
Click to see CD Hierarchy help
 cd11340 Branch
 Whole Hierarchy
 [Download CDTree]
CD Hierarchy
Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1H3G_A       104 GPGDAIYQIXPDRFANGDPSNDNVAgxr-eqADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDa------- 175
3EDF_A       104 GPGDAIYQIMPDRFANGDPSNDNVAgmr-eqADRRHGGGRHGGDIRGTIDHLDYIAGLGFTQLWPTPLVENDa------- 175
gi 83816389   87 SSEDVIYLLMPDRFANGAPENDSIPgfl-egVDRSDPDARHGGDFAGIREHLDYIDDLGMTALWMTPIFENDmp------ 159
gi 94968530  121 NASDTIYLIMPDRFADGDPSNNDPQnak-ghYDRAKQMAYHGGDLKGVTDHLDYLHDLGVSTVWLTPWWKNDg------- 192
gi 225874090 137 SAADTMYLIMTDRFADGDLSNDPHP------SQLALPRGWHGGDFKGIQDHLNYLKQLGITTIWITPAYDNSg------- 203
gi 254444955 121 DSSDLIYLMMPDRFANGNTENDNVEglt-etVDRSDPTKRQGGDIQGISDHLDYIDELGMTAIWFTPMFENNsp------ 193
gi 256424069 126 NSSDFVYLIMPDRFANGDKNNDVIKgmqetsLNRDSMYKRHGGDIQGIIDHLGYLQQMGVTALWMTPLVTNDq------- 198
gi 284037765 128 TAADFIYLIMPDRFANGDPSNDKFPdmldtqADTKNPYLRHGGDFTGIINHLDYLKDLGVTALWLTPVIDNDetlkkegp 207
gi 301164079 121 DASDALYLLMPDRFANGNPDNDRIEgmaeykVDRNDPNARHGGDLAGIEQNLDYFTGLGVTALWFTPVLENNm------- 193
gi 312886696 124 TSKDLIYLIMPDRFSNGDPSNDSKPgmletaVNRDSIYYRHGGDIQGVMNHLDYLKDLGVTTIWLTPEIENDe------- 196
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               # #                                       #                              
1H3G_A       176 --AAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGXGLIQDVVLSHIGKHHWWXKDLPTPDWinyggkfvp---tq 250
3EDF_A       176 --AAYSYHGYAATDHYRIDPRYGSNEDFVRLSTEARKRGMGLIQDVVLSHIGKHHWWMKDLPTPDWinyggkfvp---tq 250
gi 83816389  160 -pEYGAYHGYAATDMYRVDPRFGSNDTFRRLVESAHERDLKVIMDMIHNHIGDRHWWMDDPPTGDWvhdfdkygt---tn 235
gi 94968530  193 --NSADYHGYHVTDFYGIEDHFGNMKDLQQMVSAAHGKGMKVLMDYVVNHTGPFHPWAEHPPTPTWlhgtpakhpq--pk 268
gi 225874090 204 --GQQDYHGYSATNMYKPDPHFGSIRDFENLVSAVHADGMKFVLDTVPNHVGAANPWALDPPAPGWfhgtvahhde--ak 279
gi 254444955 194 -pSYGGYHGYAATDMYNVDRRVGSNEAYKQLVTDVHARGMKVIMDMIHNHIGLDHWWMSDLPTKDWihdveeygy---tn 269
gi 256424069 199 --PSASYHGYAATENYRIDPRFGSNELYKVLADSLHKRGMKLVQDLVHNHIGSQHWTMKDLPMKNWvhqwpaftr---ss 273
gi 284037765 208 drNQAGYHGYHFTDHYQIDKRFGGIAGYVELASALHKRGMKLVQDAVYNHISDDHWFFKDKPMKDWvnvwptytg---st 284
gi 301164079 194 --KGGSYHGYATTDYYKVDPRFGTNEEYRSLIAKAHNRGIKVVMDMIFNHCGVEHPWIKDMPSKDWfnhadfknnfvqts 271
gi 312886696 197 --PQASYHGYAVTDHYKTDPRYGNNQLYKQYVEKCHAIGLKVIKDLVHNHVGTEHWFIKDMPMKSWvhqwptytq---sn 271
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                               ##  #                              # ##  #               
1H3G_A       251 hhrvavqDPYAAQADSENFTKGWFVEGXPDLNqtnpLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLXA 330
3EDF_A       251 hhrvavqDPYAAQADSENFTKGWFVEGMPDLNqtnpLVANYLIQNNIWWIEYAGLSGLRIDTYGYSDGAFLTEYTRRLMA 330
gi 83816389  236 yegaaviDPYAAEHDREQLTDAWFVPSMPDLNqdneLLATYLIQNTLWWIESTGIDGIRMDTYFYADKDYMTRWTSAVLE 315
gi 94968530  269 ynfwplvDPHGTQADRTPVLEGWFVDRLPDLNvddpKLTEYLIDNGLWWMETASLDGYRLDTFPYSSREFWSKWHKALFE 348
gi 225874090 280 snfeaitDPHSDWAQRKDITEGWFANVLPDLNqenpLVSQYLTQNALWWIETGGLDGLRIDTFPYVGRAFWQHFNGEIHQ 359
gi 254444955 270 fkgtiqgDPNASQYDKEKLVKGWFVPYMPDLNqrndLLADYLIQNSIWWIEYSGIDGIRMDTYLYPYPEYMSRWVSEVLA 349
gi 256424069 274 fraaplmDPYAAPSDQKIMTDGWFDLHMPDMDqknpYVRRYFTQSHIWWIEYAGVDAFRLDTYPYNDADFMSEWGKAIKA 353
gi 284037765 285 hkeqslyDPHGATADKKTLLDGWFTPFLPDLNqrnpFVANFLIQHAIWSTEMFSLDAWRIDTYKYNDLDFLNRCNKALMD 364
gi 301164079 272 ykltphvDPYASEYDFDQMNNGWFVEAMPDLNqknpHVYKYLLQNSLWWIEYADIDGIRMDTYPYADYDAMSNWMKELNE 351
gi 312886696 272 frdaavmDPHASPVDRKTMLDGWFDHRMADMNesnpYVQNYLTQNHIWWIEYAGVDGFRLDTYPYNDAAYMADWARKIKA 351
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                 # #                                                                    
1H3G_A       331 EYPRLNXVGEEWSTRVPvvarwqr-gkanfdGYTSHLPSLXDFPLVDAXRNalsktg--eenglNEVYETLSLDYLYPEP 407
3EDF_A       331 EYPRLNMVGQEWSTRVPvvarwqr-gkanfdGYTSHLPSLMDFPLVDAMRNalsktg--eenglNEVYETLSLDYLYPEP 407
gi 83816389  316 EYPDFNIVGESWVPTVPheaywqddfqahpdDYDSDLPSVTDFPLSFAMQDafapd----gggvYDLYRTLAQDHVYPAP 391
gi 94968530  349 VYPRTFTIGEVSDGDPAvvsffqg-grkeydGIDSGVTTVFDFPTMYAIRDvlir-----qqpaSKLQEVLEHDALYPNP 422
gi 225874090 360 VFPRVTEVGEVFNPDPTivsyfa--ggvahdGIDTHLYTPFDFPTYFALRAvlth-----qkpmSYLESVWGKDWLYPHP 432
gi 254444955 350 AYPNFNIVGEVWVETVAhesywqd-dsknadGYDSELPSVTDFPLSFAIRNglneef-gwetglSRIYYAFAQDRLYTDP 427
gi 256424069 354 AYPGFTFFGEVWVHSGPeqvfftq-gntvnrGFDTNLPGTTDFQSLWAISAalnekp-gwddgvVKLYATLIQDYQYQDP 431
gi 284037765 365 EYPKIHLFGESVVNNPVgqaffv--kntvgfPFKSNQPGALDFVLYNAFNDalnqrf-dwdsgvNRIHQVLAQDDVYADP 441
gi 301164079 352 EYPNYNTVGETWVTEPAytawwqk-dsklsaPRNSHLKTVMDFSFFDKVNTakneqtdtwfkglDRVYNNFVYDYLYPNP 430
gi 312886696 352 EFPHFSIFGETLVWSVPnqayftq-gntvnrGFDTHLPGITDGQIKDGIFEalngkd-gwtdgvNRLYSILAQDFLYQDA 429
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                 ##                                                                     
1H3G_A       408 QNLVLFGGNHDxarxfsaagEDFDRWRXNLVFLXTXPRIPQFYSGDEIlxtstvkgrddasyRRDFPGGWAGDKANAFSG 487
3EDF_A       408 QNLVLFGGNHDmarmfsaagEDFDRWRMNLVFLMTMPRIPQFYSGDEIlmtstvkgrddasyRRDFPGGWAGDKANAFSG 487
gi 83816389  392 NKLVTFLDNHDltrffsvvdEDEDAFKLAYAFLMTTRGIPQVYYATELmqpmldv-egdgakRPDMPGGWPGDARSVFTE 470
gi 94968530  423 AVLVPFIGNHDkprfmgekgATVPELNAAASLLLTLRGIPQLYAGDEIampgg----edpdnRRDFPGGFAGDPQNAFTA 498
gi 225874090 433 NRLVPFFGNHDtmrfmslpgMTVADLKLAYGIVLTMRGMPEIYYGDELamkgg----ddpnnRHDFPGGFPGGKRDAFTR 508
gi 254444955 428 NNNVIFIDNHDmsrvyehlgKDEDLFKIAYSVLLTARGIPQVYYGTELmmehenrggddeawRQTMPGGWPDDDRNVFKK 507
gi 256424069 432 MRNVVFLDNHDlsrfysvvkENKNKYKAALAWLLTTRGIPQLYYGAEIgmknfs--apdglvREDFKGGWTGDTQNKFTA 509
gi 284037765 442 NKLVTFLENHDtdrylsvigEDFDKYKLGVTWLLTTRGIPHWYYGTEIlmkgtkn-psdaevRKDFPGGFPGDKENKFEA 520
gi 301164079 431 ASVLAFIENHDtdrf-lgegENLDMLKQASTLLLTTRRIPQLYYGTEVmmngvks-ksdgyvRKDFPGGWADDKENALTP 508
gi 312886696 430 TRNVVFLDNHDmsrfysmvnEDFSKFKAGMALLLTMRGIPQLYYGDEIlmknfs--npdglvRLDFPGGWAGDKSNKFTQ 507
                        410       420
                 ....*....|....*....|...
Feature 1                               
1H3G_A       488 AGLtsQQRAAQDLVRKLANWRKN 510
3EDF_A       488 AGLtsQQRAAQDLVRKLANWRKN 510
gi 83816389  471 EGRtaRENRAHDFVTTLTTWRED 493
gi 94968530  499 SGRtpEQQEAFAHLQKLLQLRKQ 521
gi 225874090 509 AGRtpKENEVHDWVAGLLHFRDT 531
gi 254444955 508 SGRteKENEILSYMKKMNEWRKQ 530
gi 256424069 510 GGRnaEENELFNYVSTIANYRKN 532
gi 284037765 521 AGRtdRENEAVQYVRKLATYRRN 543
gi 301164079 509 EGRtrLQNESYNFYRNLLNWRKG 531
gi 312886696 508 DGRtgKENEAFNYVRALANFRKQ 530

Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
Click on image for an interactive view with Cn3D
Conserved site includes 14 residues -Click on image for an interactive view with Cn3D