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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN-LIKE MITOCHONDRIAL PEPTIDE DEFORMYLASE IN COMPLEX WITH ACTINONIN
 
Authors :  S. Fieulaine, T. Meinnel, C. Giglione
Date :  26 Feb 13  (Deposition) - 26 Feb 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peptide Deformylase, Mitochondrial, Actinonin, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fieulaine, M. Desmadril, T. Meinnel, C. Giglione
Understanding The Highly Efficient Catalysis Of Prokaryotic Peptide Deformylases By Shedding Light On The Determinants Specifying The Low Activity Of The Human Counterpart.
Acta Crystallogr. , Sect. D V. 70 242 2014
PubMed-ID: 24531459  |  Reference-DOI: 10.1107/S1399004713026461

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 1A, CHLOROPLASTIC/MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 79-267
    Gene: AT1G15390, DEF, DEF1, F9L1.34, F9L1_34, PDF1A
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATDEF1, ATPDF1A, PDF 1A, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:46 , CYS A:47 , VAL A:48 , GLY A:49 , GLN A:54 , ARG A:84 , GLY A:110 , CYS A:111 , GLU A:112 , TRP A:146 , HIS A:153 , GLU A:154 , HIS A:157 , ZN A:202 , HOH A:463 , HOH A:567BINDING SITE FOR RESIDUE BB2 A 201
2AC2SOFTWAREGLN A:54 , CYS A:111 , HIS A:153 , HIS A:157 , BB2 A:201BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWAREPRO B:46 , CYS B:47 , VAL B:48 , GLY B:49 , GLN B:54 , ARG B:84 , GLY B:110 , CYS B:111 , GLU B:112 , ARG B:118 , TRP B:146 , ARG B:149 , HIS B:153 , GLU B:154 , HIS B:157 , ZN B:202 , HOH B:351 , HOH B:403 , HOH B:425BINDING SITE FOR RESIDUE BB2 B 201
4AC4SOFTWAREGLN B:54 , CYS B:111 , HIS B:153 , HIS B:157 , BB2 B:201BINDING SITE FOR RESIDUE ZN B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JE7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:45 -Pro A:46
2Ala B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JE7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JE7)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4je7a_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhh..hhhhhhhh....eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.....ee.hhh...........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4je7 A   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPCVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCESVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSHHH 194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains d4je7b_ B: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhh.hhhhhhhh....eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh......ee.hhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4je7 B   3 LPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPCVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCESVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGS 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JE7)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DEF1A_ARATH | Q9FV53: 1zxz 1zy0 1zy1 4je6 4je8

(-) Related Entries Specified in the PDB File

4je6 4je8