3.5.1.88: peptide deformylase
This is an abbreviated version!
For detailed information about peptide deformylase, go to the full flat file.
Word Map on EC 3.5.1.88
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3.5.1.88
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actinonin
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medicine
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n-formylated
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deformylation
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eubacteria
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hydroxamic
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drug development
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formyltransferase
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oxazolidinone
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catarrhalis
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linezolid
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moraxella
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hexxh
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biotechnology
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synthesis
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agriculture
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molecular biology
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analysis
- 3.5.1.88
- actinonin
- medicine
-
n-formylated
-
deformylation
- eubacteria
-
hydroxamic
- drug development
-
formyltransferase
-
oxazolidinone
- catarrhalis
- linezolid
- moraxella
-
hexxh
- biotechnology
- synthesis
- agriculture
- molecular biology
- analysis
Reaction
Synonyms
AtDEF1.1, AtDEF1.2, AtDEF2, AtPDF1A, AtPDF1B, AtPDF1Bt, AtPDF2, BbPDF, BcPDF, BcPDF2, DEF, Def1, DEF2, deformylase, peptide N-formylmethionine, EC 3.5.1.27, EcPDF, ECPDF1B, EfPDF, HpPDF, HsPDF, hydrolase, aminoacyl-transfer ribonucleate, LiPDF, mPDF, Ni-peptide deformylase, PDF, PDF-1, PDF-2, PDF1A, PDF1B, PDF2, PdfA, PdfB, PdfC, peptide deformylase, peptide deformylase 1, peptide deformylase 1A, peptide deformylase 1B, peptide deformylase 2, Pf PDF, PfPDF, Polypeptide deformylase, SaPDF, sPDF, TbPDF1, TbPDF2, type I PDF, type II PDF, type II peptide deformylase, Vp 16 PDF1B, Vp16 PDF, Vp16T, XOO1075, XoPDF
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Subunits
Subunits on EC 3.5.1.88 - peptide deformylase
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dimer
monomer
multimer
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mPDF in solution shows a molecular mass of 100 kDa, several mixed fractions of different mutants display enzyme activity
additional information
additional information
comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview
additional information
comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview. Detailed analysis of the three-dimensional structure of human PDF with bound Co2+
additional information
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comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview. Detailed analysis of the three-dimensional structure of human PDF with bound Co2+
additional information
comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview. The subunit structure of PfPDF consists of a mixed alpha/betatopology, with three anti-parallel beta-sheets, three major alpha-helices, and one small helix near the N-terminus
additional information
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comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview. The subunit structure of PfPDF consists of a mixed alpha/betatopology, with three anti-parallel beta-sheets, three major alpha-helices, and one small helix near the N-terminus
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additional information
comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview
additional information
the core of SaPDF is composed of two alpha-helices, three 310-helices and eight beta-strands organized in two beta-sheets. In addition, SaPDF contains the typical insertions of type 2 PDFs, including an eight-amino acids loop folded as an alpha-helix and a long loop connecting strands beta2 and beta3 usually referred as the CD-loop. It also displays the classical C-terminal extended fold of type 2 PDFs. The structure is organized into two subdomains around the active site, called N- and C-terminal subdomains
additional information
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the core of SaPDF is composed of two alpha-helices, three 310-helices and eight beta-strands organized in two beta-sheets. In addition, SaPDF contains the typical insertions of type 2 PDFs, including an eight-amino acids loop folded as an alpha-helix and a long loop connecting strands beta2 and beta3 usually referred as the CD-loop. It also displays the classical C-terminal extended fold of type 2 PDFs. The structure is organized into two subdomains around the active site, called N- and C-terminal subdomains
additional information
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the core of SaPDF is composed of two alpha-helices, three 310-helices and eight beta-strands organized in two beta-sheets. In addition, SaPDF contains the typical insertions of type 2 PDFs, including an eight-amino acids loop folded as an alpha-helix and a long loop connecting strands beta2 and beta3 usually referred as the CD-loop. It also displays the classical C-terminal extended fold of type 2 PDFs. The structure is organized into two subdomains around the active site, called N- and C-terminal subdomains
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additional information
the C-terminal extremity of Vp16 PDF revealed that it is tightly bound to the globular core of the protein involving (i) a hydrogen bond made between the side chains of the penultimate residue, Thr136, and that of Tyr88 located immediately after motif II (m2, composed of residues 83-87) and (ii) a salt bridge between the C-terminal carboxyl group of the last residue, Ile137, and the side chain of Lys91, with both amino acids sitting in a structured loop between strands beta4 and beta5. In addition, the side chain extremity of Lys95 is within hydrogen bonding distance of the carboxyl terminal of Ile137. The side chain of Ile137 is clamped by residues coming from beta4 and beta5 strands and their connecting loop, especially by Tyr88, Lys91, Val93 and Lys95 side chains