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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN-LIKE MITOCHONDRIAL PEPTIDE DEFORMYLASE IN COMPLEX WITH MET-ALA-SER
 
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 :  2.40
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Peptide Deformylase, Mitochondrial, Hydrolase-Peptide 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
 
Molecule 2 - TRIPEPTIDE MET-ALA-SER
    Chains: D, E
    Engineered: YES
    Other Details: CHEMICAL PRODUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:54 , CYS A:111 , GLU A:112 , HIS A:153 , HIS A:157 , HOH A:301BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS B:111 , GLU B:112 , HIS B:153 , HIS B:157 , HOH B:301BINDING SITE FOR RESIDUE ZN B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JE8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 4JE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JE8)

(-) Exons   (0, 0)

(no "Exon" information available for 4JE8)

(-) Sequences/Alignments

Asymmetric 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh............hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhh..hhhhhhhhh...eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh......ee.hhh...........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4je8 A   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPCVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCESVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSHH 193
                                    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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh............hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhh.hhhhhhhh....eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhhh.hhhhh......ee.hhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4je8 B   3 LPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPCVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCESVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGS 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         


Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4je8 D   1 MAS   3


Chain E from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4je8 E   1 MAS   3
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4JE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JE8)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  3.5.1.88
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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 4je7

(-) Related Entries Specified in the PDB File

4je6 4je7