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1def

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PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES

Structural highlights

1def is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEF_ECOLI Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Escherichia coli peptide deformylase, a member of the zinc metalloproteases family, is made up of an active core domain composed of 147 residues and of an additional and dispensable C-terminal tail of 21 residues. The three-dimensional structure of the catalytic core could be studied by NMR. 1H and 15N NMR resonances assignments were obtained by two-dimensional and three-dimensional heteronuclear spectroscopy. The structure could be calculated using a set of 1015 restraints for the 147 residues of the enzyme. The overall structure is composed of a series of antiparallel beta-strands which surround two perpendicular alpha-helices. The C-terminal helix contains the HEXXH motif, which is crucial for activity. This helical arrangement and the way the histidines bind the zinc ion clearly are structurally reminiscent of the other members of the metalloprotease family, such as thermolysin or metzincins. Nevertheless, the overall arrangement of secondary and tertiary structures of peptide deformylase and the positioning of its third zinc ligand (a cysteine) are quite different from those of the other members of the family. These discrepancies, together with several biochemical differences, lead us to propose that peptide deformylase is the first example of a new class of the zinc-metalloproteases family. Studies of the interaction of peptide deformylase with either an inhibitor of the reaction or a product of the catalysed reaction, Met-Ala-Ser, as well as comparisons with the structures of other enzymes of the family, have enabled us to delineate the area corresponding to their binding site. The structural basis of the specificity of recognition of the formyl group is discussed in the context of the protease superfamily.

A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase.,Meinnel T, Blanquet S, Dardel F J Mol Biol. 1996 Sep 27;262(3):375-86. PMID:8845003^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Meinnel T, Blanquet S, Dardel F. A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase. J Mol Biol. 1996 Sep 27;262(3):375-86. PMID:8845003 doi:http://dx.doi.org/10.1006/jmbi.1996.0521

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1def"

Categories: Escherichia coli | Large Structures | Dardel F | Meinnel T

@@ Line 1: / Line 1: @@
 ==PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES==
-<StructureSection load='1def' size='340' side='right'caption='[[1def]], [[NMR_Ensembles_of_Models | 9 NMR models]]' scene=''>
+<StructureSection load='1def' size='340' side='right'caption='[[1def]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1def]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DEF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1def]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DEF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1def FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1def OCA], [https://pdbe.org/1def PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1def RCSB], [https://www.ebi.ac.uk/pdbsum/1def PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1def ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
+[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Formylmethionine deformylase]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Dardel, F]]
+[[Category: Dardel F]]
-[[Category: Meinnel, T]]
+[[Category: Meinnel T]]
-[[Category: Hydrolase]]
-[[Category: Zinc metalloprotease]]

1def

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Current revision

PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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