2E2L,3DLA,3DLA,3DLA,2E2L,2E11,2E11,1EMS,1J31,1J31,1UF8,1FO6,1FO6,2VHI,3HKX


Conserved Protein Domain Family
nitrilase

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cd07197: nitrilase 
Click on image for an interactive view with Cn3D
Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes
This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy.
Statistics
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PSSM-Id: 143587
View PSSM: cd07197
Aligned: 145 rows
Threshold Bit Score: 73.8979
Threshold Setting Gi: 117648
Created: 30-Sep-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:2E2L_A; Helicobacter pylori formamidase (HpAmiF, C166S mutant) monomer bound with formamide, contacts calculated at 4 A.
    View structure with Cn3D
  • Structure:3DLA_C; Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase (GAT_Gln-NAD-synth) monomer bound with DON inhibitor in the GAT domain, contacts calculated at 4 A.
    View structure with Cn3D
  • Comment:M. tuberculosis GAT_Gln-NAD-synth is a bifunctional enzyme having a NAD+ synthetase domain in addition to this GAT domain.
  • Structure:1J31_A; Pyrococcus horikoshii hypothetical protein Ph0642 bound with acetate; contacts calculated at 4A.
    View structure with Cn3D
  • Structure:1UF8_A, Agrobacterium sp., N-carbamyl-D-amino acid amidohydrolase (DCase, C171aV236A mutant) homodimer bound with N-carbamyl-D-phenylalanine; contacts defined at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                     #                                  
2E2L_B        16 VAAIQFPvpivn-srkdIDHNIESIIRTLHATkagypgVELIIFPEYSTQglntakwlse-------------eflldvp 81  Helicobacter py...
ZP_00990682    3 FALLQFPis------akSTDNYQTIKRAICEAse--ndAQVLLTQECALSgyppveissvs------------didfeqq 62  Vibrio splendid...
NP_147881      3 IAILHSRvkl-----aaKRSNARRHSILIDKVvst-rtVDLIVLPAYPFTgpligyyppskarlklrelaekiseknipa 76  Aeropyrum perni...
YP_001012561   5 VALTHMKlrp-----laKKSNLEKARKLVREAal--kgAKLVVLPSFVNIghfflhyprtrsra------itrnqaerip 71  Hyperthermus bu...
NP_376244      3 IGLLHLRlke-----msKKYNIEKAKKLIKAAkd--kgAKLVILPSLFPAgnifeiyendkksk-----siiknlaekip 70  Sulfolobus toko...
YP_001041124  26 IAIGHLNvyi-----rdKRNNLDVARKSLLLAhe--nyVDTLILPYMQPYgpildnniskstl--------rkkyglslt 90  Staphylothermus...
NP_354651     43 VAVAQTSlfndprdvsaLKTCGNEIRRLMGNAhn--agTRLIHFPEGATCwphkrimsetgpreig--padwtrfewktl 118 Agrobacterium t...
YP_001978743  45 VAAAQTFvs------adIAANGRGIRKLISSAaa--qgVRLISFCEGTLSgygkfqimaqdd---------wqtydwaaq 107 Rhizobium etli ...
YP_431519      3 IALASPPip------ksVDNALQWVDRLVTEAtl--skVDLICFPEAYVPgirgmdfkve-------------ncsprkm 61  Hahella chejuen...
ZP_04359665    3 VALASPPfp------ksLQDGLFWLEKLVKEAaa--asAAIICFPESYLPgypgmgyap----------------edrsr 58  Chitinophaga pi...
Feature 1                                                                    #   #    #          
2E2L_B        82 gkeTELYAKACke---aKVYGVfSIM------ERnpdsnknpYNTAIIIDPQGeiiLKYRKLFPWn-pIE---PWYPGDl 148 Helicobacter py...
ZP_00990682   63 diaFNEIIELVke---kQIYLFlGCIrq--cgERa-------ANSIAIIEPSGy-vQYYDKRALWgwdAD---NFVVDSn 126 Vibrio splendid...
NP_147881     77 gpsVSFMSRWSqe---yGVYILgGPIi-----ERagp---riYVTTVLTSPDGsiaGKYRKVSLTeeeRDm--GISPGKe 143 Aeropyrum perni...
YP_001012561  72 gntFEYLSMVAle---nGVYIIaGPIi-----ERagp---kiFLTTMVISPNGsliAKYRKVASNgldEEl--GISPGKq 138 Hyperthermus bu...
NP_376244     71 gsvTDTLINLSme---gEIHLIaGPIl-----EQagp---kiFLTTLIISPQGeilGKYRKIIVSe--KDvrlGISAGKe 137 Sulfolobus toko...
YP_001041124  91 sgyLASLSIIAkn---yGVNVLlMSTi-----EKags--kiyVTAFLIPGIIGepiEKYRKIVLSd--REkiiGFNKGKt 158 Staphylothermus...
NP_354651    119 reeLEAIRKLArk---lKLWTVlGAIhqltppHRp-------YNSLYVISDRGtliTRYDERLLSk-tKIs-fMYSPGRl 186 Agrobacterium t...
YP_001978743 108 daeLRAIAELCgk---lRIFAVvGGA------HRlsng-hppHNSLYVLSERGaliTRYDKRFLSn--SElggWYTPGTq 175 Rhizobium etli ...
YP_431519     62 qsaLDRICDLArk---tSINIIlPMEwp--apEGr-------RNVAFVVDRRGvllGKQTKNHLEq-gEEa--YFIPGAr 126 Hahella chejuen...
ZP_04359665   59 kslLHALAKVCdiaaehAITIIvPMDwy--idEQl-------VNLAFVVSAKGevlGYQTKNQLDp--TEd-eLWTAGTt 126 Chitinophaga pi...
Feature 1                            ## ##                      #                                
2E2L_B       149 gmPVCEGpg---gsKLAVCISHDGMIPEl-AREAAyk-gCNVYIRISGystqv---------------ndqwILTNRSNA 208 Helicobacter py...
ZP_00990682  127 fnGVVEIkg----iRIGVRVCYEIRFPEy-FRELYke-kVDVTVVCLCdvqdkpd----------dnrlsiiKSHLVSRA 190 Vibrio splendid...
NP_147881    144 -pGIFKLkvngsdvSLGVFSDEDLATPEi-FRHLQlg-gSKIIVGTIFpynssflggiiddeglvtmdhtvvKTFLEVRS 220 Aeropyrum perni...
YP_001012561 139 -tVVIDDig----rSIGVMAEDDILYPEi-ARSLLle-gATALIVTLRpged----------------vnrvKLALMARS 195 Hyperthermus bu...
NP_376244    138 --PVYMSld----kRYGIISEDDIFSPEi-NRLLSlnnvAAIVGTVKAyprng---------------ydiiKYMAIART 195 Sulfolobus toko...
YP_001041124 159 -iKKFRCrn----iYYSIVLDDEILYPE--LAKLNlylgTDILFVGIApdyp----------------vknyMSIIKSLA 215 Staphylothermus...
NP_354651    187 -pVTFEVdc----fRFGCALGMEAHYPEi-FMEYEkl-nVDCVLFSTAgedas--------------nahafAAEILGHA 245 Agrobacterium t...
YP_001978743 176 -pIIFEVds----yRFGCAICIESQFEEv-FREYErl-gVDGVLFSSYgia------------------pyfQIALRAHA 230 Rhizobium etli ...
YP_431519    127 -rQLFDAdg----vKFGIVISHEGWRCPetVRWAAsr-gAKIVFHPHFtgshfkgvklt---qwgklenpfyERAMQCRA 197 Hahella chejuen...
ZP_04359665  127 -rSIFDVng----vKFGITICHEGFRYPesVRWAAqq-dAKIVFMPHFggsetagpelk---ewgakenpyyEKAVMLRA 197 Chitinophaga pi...
Feature 1                                                                                        
2E2L_B       209 WHN-LMYTVSVNlagydn-vfyyfGEGQICNFd------GTTLVQGHrn-pwEIVTGEIYPK------MADNARlswgle 273 Helicobacter py...
ZP_00990682  191 IEN-VFTVISVNsstl-----eqtAPTSVIDQh------GNTLVQTVrn-seSITYYTYEKIe-----NGFGAKg----- 247 Vibrio splendid...
NP_147881    221 RET-GVPIILVGsiidsgvetlayMSTIPVEPd-----eGVIEDKMFgp--dDESPIFIDLNe-----KATNPRkpp--- 284 Aeropyrum perni...
YP_001012561 196 IEN-NVPILAVGsvfeaa-ervveIPTMVVDPq-----nGIVEEVNEpn--dTYILVEVMEQps---nIQDIVRts---- 259 Hyperthermus bu...
NP_376244    196 IENgLPYIIVGEtie------denGEIIGSSPtfvtsvnSLIYKQAEe---eDTVVYVESTVlt---qEAGRERigs--- 260 Sulfolobus toko...
YP_001041124 216 LMT-RSKIVLVGgiyy-----yenKLSYIVPTiil-dqrGNVLFKYIs---dEQALIMLPTQy-----LIRENKkid--- 277 Staphylothermus...
NP_354651    246 ASN-TYWVSYSTlaaq-----spgAPSGIAAPd------GQWVAQCPmnglpAIALADVIIDre---hPARPWRq----- 305 Agrobacterium t...
YP_001978743 231 GLN-CIWIIAATpvqk-----ahkGPAGVIGPd------GDWAARCAalpepDFAMAMLDRNdaaydiPLQKARpw---- 294 Rhizobium etli ...
YP_431519    198 IEN-TVFFASVNyamd-----yqgSATTLIAPd------GACVAYQPya-evGALVINIDVRda---tGVNARRy----- 256 Hahella chejuen...
ZP_04359665  198 MEN-TIYTASSNyasp-----ytdAASTLVAPd------GSCVAHEAyg-rvGVVVAEIDPE------KASGLLa----- 253 Chitinophaga pi...
Feature 1               
2E2L_B       274 nniYNLG 280 Helicobacter pylori 26695
ZP_00990682  248 --lIKYS 252 Vibrio splendidus 12B01
NP_147881    285 -ehLKIL 290 Aeropyrum pernix K1
YP_001012561 260 -lmAKAL 265 Hyperthermus butylicus DSM 5456
NP_376244    261 innIDSV 267 Sulfolobus tokodaii str. 7
YP_001041124 278 -qeTMFI 283 Staphylothermus marinus F1
NP_354651    306 ---KART 309 Agrobacterium tumefaciens str. C58
YP_001978743 295 -raKARQ 300 Rhizobium etli CIAT 652
YP_431519    257 --aPERD 261 Hahella chejuensis KCTC 2396
ZP_04359665  254 ---KRFK 257 Chitinophaga pinensis DSM 2588

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