1G27,1N5N,1BS4,1LQW,1RL4,1LQY,1LM6


Conserved Protein Domain Family
Pep_deformylase

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cd00487: Pep_deformylase 
Click on image for an interactive view with Cn3D
Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents.
Statistics
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PSSM-Id: 238271
Aligned: 155 rows
Threshold Bit Score: 116.817
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1G27; type I PDF of E. coli with bound inhibitor BB-3497 and metal ion; contacts at 3.5A
  • Structure:1LQY; type II PDF of B. stearothermophilus with bound inhibitor actinonin and metal ion: contacts at 3.5A
  • Citation:PMID 9126850

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                   ###    #                            
1G27_A        5 VLHIPDERLRKVAKPVeevn---aeiQRIVDDMFETMYAE---EGIGLAATQVDIHQRIIVIDVsenrDERLVLINPELL 78  Escherichia coli
AAQ57593     70 IVQLPARSLWCKQYPLdislvrrgefNDMIGRVRAARHYY---QYPSLCAPKIGWNVQMFTLFDg---TVFINPINLDAL 143 Trypanosoma brucei
AAG09295     42 VACYPHRSLTRPALRLerhq---vntPLFHSQLLNLNKMAtdlQCISFSAPKGHWDAAIVLIKGhpneANFEVWVNPTVP 118 Trypanosoma brucei
NP_561676     4 PIVKDVLFLGQKSELAtk------edIGIIDDLVDTLRANl-eSCVGMAANMIGVKKRILVFSIg---NIIVPMVNPVIL 73  Clostridium perf...
ZP_00333082   4 PIMKDIFFLQQKSEPAtq------ldVQVGQDLQDTLSANa-hACVGMAANMIGIKKRIIIVNMg---FTNLVMYNPVLI 73  Streptococcus su...
NP_735841     4 PIVRDTFFLQQKSQMAsr------adVSLAKDLQDTLHANq-nYCVGMAANMIGSLKRVIIINVg---ITNLVMFNPVLV 73  Streptococcus ag...
NP_786276     4 PIVHDPAALSVPADLAtp------adTQVLTDLLDTLAAHt-dNCVGMAANMIGVNKQIIVVQLg---PFAIAMINPKII 73  Lactobacillus pl...
ZP_00323653   4 SVIHDQQILSQTSIPAtk------qdLSVVMDLMDTLKANs-eRCVGMAANMIGVHKRIIVVTMg---MMNVPMINPVIL 73  Pediococcus pent...
NP_359001     4 KIVKDILFLSQVSQPAsq------edLYLARDLQDTLLANr-dTCVGLAANMIGVQKRVIIFNLg---LVPVVMFNPVLL 73  Streptococcus pn...
AAN25486      4 PIMTSRSFLRTPSEAAgp------gdEQVIEDLVDTLEANr-sRCVGMAANMIGVGKRIIVFVDedlgGRITVMLNPVIT 76  Bifidobacterium ...
Feature 1                                           ###                                        #
1G27_A       79 e------------------------kSGETGI--EEGCLSIPEqralVPRAEKVKIRALDRDGKPFELEADGLLAICIQH 132 Escherichia coli
AAQ57593    144 eveeiakqksitfveaealwmekkrrEGKTCFa-WEPCASCCFllhfIERPSTVRVRAIAEDGNPFEVTLDKMRARMALH 222 Trypanosoma brucei
AAG09295    119 gyd--------------------drhSIAPMYgmWENCISCGActawVIRPQSITCSGLDEYGNEKTEVLDGMRARCLMH 178 Trypanosoma brucei
NP_561676    74 k------------------------kEKSYET--EESCLSLTGfr-kTTRYEIIEVEYLDRNFKKHKETFSGFTAQIIQH 126 Clostridium perf...
ZP_00333082  74 s------------------------kAKPYQT--EEGCLSLEGtr-pTTRYQEIEVEFLDASWKKISLKLTDFQAQIVQH 126 Streptococcus su...
NP_735841    74 a------------------------kSDPYET--EESCLSLVGcr-sTQRYRHITISYRDINWKEQQIKLTDFPAQICQH 126 Streptococcus ag...
NP_786276    74 d------------------------hHGTYET--KEGCLSLPGer-pTSRYHQITVKYKDQHFKPQQQRFNDFTAQIIQH 126 Lactobacillus pl...
ZP_00323653  74 k------------------------kGNPYTT--EEGCLSLTGer-sTTRYDEIEVQYLDLEFKKHTQEFKEFIAQIIQH 126 Pediococcus pent...
NP_359001    74 s------------------------fEGSYEA--EEGCLSLVGvr-sTKRYETIRLAYRDSKWQEQTITLTGFPAQICQH 126 Streptococcus pn...
AAN25486     77 a------------------------sDGAFDT--QEGCLSLTGer-rTLRYRRIEVNYENRRFRARHATFAGWTAQIIQH 129 Bifidobacterium ...
Feature 1       #  #      
1G27_A      133 EMDHLVGKLF 142 Escherichia coli
AAQ57593    223 ELDHLNGILF 232 Trypanosoma brucei
AAG09295    179 ELDHLSGKTI 188 Trypanosoma brucei
NP_561676   127 EVDHFEGIII 136 Clostridium perfringens str. 13
ZP_00333082 127 ELDHLEGIII 136 Streptococcus suis 89/1591
NP_735841   127 ELDHLEGILI 136 Streptococcus agalactiae NEM316
NP_786276   127 ELDHCAGKLI 136 Lactobacillus plantarum WCFS1
ZP_00323653 127 EVDHCDGIII 136 Pediococcus pentosaceus ATCC 25745
NP_359001   127 ELDHLEGRII 136 Streptococcus pneumoniae R6
AAN25486    130 EVDHCNGIII 139 Bifidobacterium longum NCC2705

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