2E2L,2PLQ,2UXY,2E2L


Conserved Protein Domain Family
aliphatic_amidase

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cd07565: aliphatic_amidase 
Click on image for an interactive view with Cn3D
aliphatic amidases (class 2 nitrilases)
Aliphatic amidases catalyze the hydrolysis of short-chain aliphatic amides to form ammonia and the corresponding organic acid. This group includes Pseudomonas aeruginosa (Pa) AmiE, the amidase from Geobacillus pallidus RAPc8 (RAPc8 amidase), and Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and HpAmiE hydrolyze various very short aliphatic amides, including propionamide, acetamide and acrylamide. HpAmiF is a formamidase which specifically hydrolyzes formamide. These proteins belong to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 2. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. HpAmiE , HpAmiF, and RAPc8 amidase, and PaAimE appear to be homohexameric enzymes, trimer of dimers.
Statistics
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PSSM-Id: 143589
View PSSM: cd07565
Aligned: 26 rows
Threshold Bit Score: 428.629
Threshold Setting Gi: 167769967
Created: 21-Apr-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the binding of Helicobacter pylori formamidase to formamide. This subgroup also includes proteins which hydrolyze very short aliphatic amides, such as propionamide and acrylamide.
  • Structure:2E2L_A; Helicobacter pylori formamidase AmiF (C166S mutant) monomer bound with formamide, contacts calculated at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                      #                                 
2E2L_A        14 FLVAAIQFPVPIVNSRKDIDHNIESIIRTLHATKAGYPGVELIIFPEYSTQGLntaKWLSEEFLLDVPGKETELYAKACK 93  Helicobacter py...
Q887D9        15 VVIGLAQLALPDPHTREALWAQTQKVVGMVAKARRSNPGMDLIVFPEYSLHGLs--MSTAPEIMCSLDGPEVVALREACK 92  Pseudomonas syr...
YP_841971     14 VIVGLLQLRKADIATAEDLRLSAERLASFVHQVKAGRPNVDIIVFPEYSLNGAs--KALSADLQCTVDGPHVGVLRDACR 91  Ralstonia eutro...
A4Z3G9        14 VVIGLVQLQLPVVVTKEDLAKQTEKIVWMVGKARRNLGTMDLVVFPEYSLHGLs--MDTNPEIMCRLDGPEVAAFKQACI 91  Bradyrhizobium ...
EDX87233      14 VVLGMVQAQLPSVATPDDLAAQTKVICDMVAKARRNMPTMDLVVFPEYSLHGLs--MDTNPDIMCHLDGPEVTAFRQACI 91  Synechococcus s...
XP_002179811  16 VVLGMVQLQLPVIVTPGDLAEQTTRICEIVGKARRNMRTMDLVVFPEYSLQGLs--MDTRAKFMCHMEGPEVAAFKEACK 93  Phaeodactylum t...
ACO65904      16 IVLGCVQLQLPVVKTKDDLAKQTSRIVEMVGKARRNLGTMDLVIFPEYSLHGLs--MDTNPEIMCRLDGPEVQAFKAACV 93  Micromonas sp. ...
YP_887708     14 LVLGLVQARVPVIKEPGDLKSTAERLAGMVVGAKKGMPSIDLVVMPEYSINGLdpdTWLDDSLLCDRNGPEMTLLADACR 93  Mycobacterium s...
NP_947268     14 LLVAMIQYPVPVVSGPEDIQTQVKQICRAVDTTKAGYPDLDLIVFPEYSTQGLntaIWTYDEMLLTVDSPEIGAFKQACK 93  Rhodopseudomona...
CAR67550      14 LLIAAIQYPVPVIKGPEDIQIQVQQICKTIDSTKAGYPDLDIIVFPEYSTQGLntkIWTYDEMLLLLDGPEVDCFRSACI 93  Photorhabdus as...
Feature 1                                               #   #   #                        ##      
2E2L_A        94 EAKVYGVFSIMERNPdsnkNPYNTAIIIDPQGEIILKYRKLFPWNPIEPWYPGDlgMPVCEGPGGSKLAVCISHDGMIPE 173 Helicobacter py...
Q887D9        93 EHRIWGCFSIMEANPq--gNPFNSSLIVDDLGEIRLYYRKLHPWVPVEPWEPGDlgIPVCDGPRGSTLALIICHDGMFPE 170 Pseudomonas syr...
YP_841971     92 LANVWACFSFMELNPg--gNPYNSAILVNNEGQVCLHYRKLHPWVPAEPWAPGNlgIPVCEGPKGSKIAVVICHDGMFPE 169 Ralstonia eutro...
A4Z3G9        92 DNKIWGCFSIMEYNPd--gNPYNSGLIIDSNGEIKLYYRKLHPWIPVEPWEPGDlgIPVIEGPRGAKIALIICHDGMFPE 169 Bradyrhizobium ...
EDX87233      92 NNRIWGCFSIMEFNPn--gNPYNSGLIIDDDGELQLYYRKLHPWVPVEPWEPGNigIPVCDGPNGSKIALIICHDGMFPE 169 Synechococcus s...
XP_002179811  94 KHFIWGCFSIMEKNPd--gNPYNTGIIIDDKGEVKLYYRKLHPWVPIEPWEPGNigIPVCDGPNGCKLALIICHDGMFPE 171 Phaeodactylum t...
ACO65904      94 EHKIWGCFSIMEYNPd--gNPYNTGLVIDDTGKIVLYYRKLHPWIPVEPWEPGNvgIPVCNGPKGCKLALIICHDGMFPE 171 Micromonas sp. ...
YP_887708     94 DAGVWGCFSIMERNRg--gAPWNSGIIIDDHGEERLYYRKMHPWVPAEPWAPGDlgVPVCDGPSGSRLALIICHDGMLPE 171 Mycobacterium s...
NP_947268     94 RNKVWGVFSLMERNDdpslPPFNTAIIINADGELALHYRKLQPWVPIEPWSPGNygMPVCDGPKGSKLAVCICHDGMFPE 173 Rhodopseudomona...
CAR67550      94 RNDIWGVFSVMERNEdpslPPYNTAIIINNKGEIVLHYRKLQPWVPIEPWMPGNmgMPVCEGPKGSKLAVCICHDGMFPE 173 Photorhabdus as...
Feature 1                          #                                                             
2E2L_A       174 LAREAAYKGCNVYIRISGYstQVNDQWILTNRSNAWHNLMYTVSVNLAGy-DNVFYYFGEGQICNFDGTTLVQGHr-NPW 251 Helicobacter py...
Q887D9       171 MARECAYKGADIMLRTAGYtaPIRHSWKITNQSNAFTNLMQTASVCMCGs-DGTFDSMGEAMFVDFDGTIMAEGGg-RAD 248 Pseudomonas syr...
YP_841971    170 VARECAYKGAELMIRIAGYssSLRHQWHLTAQADAFCNLMYTASVCGCSa-SGPFGGMGEAIVVGFDGVPIRHGSn-KEN 247 Ralstonia eutro...
A4Z3G9       170 MARECAYKGAEIMIRTAGYtaPIRDSWRFTNQANAFQNLMVTANVCMCGs-DGSFDSMGEGMIVNFDGSILAHGTtgRAD 248 Bradyrhizobium ...
EDX87233     170 MARECAYKGADIMLRTAGYtaPIRHSWQITNQANAFCNLMVTASVCMCGt-DGTFDSMGEGMIVNFDGQPLVMGSh-RPD 247 Synechococcus s...
XP_002179811 172 MARECAYKGAEIMIRTAGYtaPIKHSWCVTNQANAFCNLMVTASVCMCGs-DGSFDSMGQGMICNFDGVPLVEGSg-RAD 249 Phaeodactylum t...
ACO65904     172 MARECAYKGAEIMIRTAGYtaPIRNSWRFTNKANSFQNLMVTANVCMCGs-DGDFDSMGEGMIVNFDGEVLSHGYsgRPD 250 Micromonas sp. ...
YP_887708    172 MAREAAYKGANVILRTAGYtyPIQHSWRITNQTNAFHNLAYTASVALAGpdQNNIWSQGEAMVCDVDGTILVSGDg-TPD 250 Mycobacterium s...
NP_947268    174 LAREAAYKGANVYIRISGYstQVNDQWIWTNRTNAWQNLMYTMSVNLAGy-DGVFYYFGEGTVCNYDGNVIQQGHr-NPW 251 Rhodopseudomona...
CAR67550     174 LAREAAYKGCNVFIRISGYstQVNDQWIWTNRTNAWQNLMYTVSVNLAGy-DEVFYYFGEGTICNYDGNVIQQGQr-NPW 251 Photorhabdus as...
Feature 1                                                             
2E2L_A       252 EIVTGEIYPKMADNARLSWGLENNIYNLGHRGYVAkpgGEHDAGLTYIKDLAA 304 Helicobacter pylori 26695
Q887D9       249 EIVCCELRPDLVREARVHWGVENNIYQFGHRGYVAvkgGARDCPYTYMRDLTA 301 Pseudomonas syringae pv. tomato str. DC3000
YP_841971    248 ELITAEIRPDLVREARRTWGAENNIYQLGHRGFVAvsgGANDCPYTYMQDLVA 300 Ralstonia eutropha H16
A4Z3G9       249 EIITAEVRPDLVREARIGWGVENNIYQLWHRGYVAvkgGAMDCPYTFMHDMVA 301 Bradyrhizobium sp. ORS278
EDX87233     248 EIITAEVRPDLVREARKHWSVENNIYQFGHRGYTAvkgGAQDCPYTYMKDMVD 300 Synechococcus sp. PCC 7335
XP_002179811 250 EIITAEVRPDLVREARVGWGVENNPYQFGHRGYVAvkgGARDCPYTYMKDMVH 302 Phaeodactylum tricornutum CCAP 1055/1
ACO65904     251 EIITAEVRPDLVREARIHWGVENNIYQFGHRGYVAvkgGATDCPYTFMKDLVD 303 Micromonas sp. RCC299
YP_887708    251 RIVTAEVVPSRADEARRTWGVENNIYQLGHRGYTAvtgGAQDCPYTFMQDLVA 303 Mycobacterium smegmatis str. MC2 155
NP_947268    252 EIVTAELFPRLVDKAREHWALENNIFNLGCRAYVGkpgGEKANYLTWVRDLAE 304 Rhodopseudomonas palustris CGA009
CAR67550     252 EIVTAELFPRLVDKARENWALENSIFNLGCRGYVGkpgGERANYLTWVRDLAN 304 Photorhabdus asymbiotica subsp. asymbiotic...

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