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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM EHRLICHIA CHAFFEENSIS IN COMPLEX WITH ACTINONIN
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  28 Sep 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ssgcid, Peptide Deformylase, Actinonin, Ehrlichia Chaffeensis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Hydrolase-Hydrolase Inhibtior Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, M. C. Clifton, T. E. Edwards, B. L. Staker
Crystal Structure Of Peptide Deformylase From Ehrlichia Chaffeensis In Complex With Actinonin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 1
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF, DEF1, ECH_0073
    Organism Scientific: EHRLICHIA CHAFFEENSIS
    Organism Taxid: 205920
    Strain: ARKANSAS
    Synonym: PDF 1, POLYPEPTIDE DEFORMYLASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2CL2Ligand/IonCHLORIDE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:111 , HIS A:153 , HIS A:157 , BB2 A:210BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARELEU A:167 , SER A:168 , LYS A:171BINDING SITE FOR RESIDUE CL A 201
3AC3SOFTWARELYS A:106 , LYS A:178BINDING SITE FOR RESIDUE CL A 202
4AC4SOFTWAREGLY A:44 , LEU A:45 , GLY A:46 , GLN A:51 , LYS A:108 , GLU A:109 , GLY A:110 , CYS A:111 , LEU A:112 , PHE A:118 , HIS A:153 , GLU A:154 , HIS A:157 , ZN A:200 , HOH A:298BINDING SITE FOR RESIDUE BB2 A 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U04)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:9 -Pro A:10
2Gly A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U04)

(-) Exons   (0, 0)

(no "Exon" information available for 3U04)

(-) 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:172
 aligned with Q2GI30_EHRCR | Q2GI30 from UniProtKB/TrEMBL  Length:188

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
         Q2GI30_EHRCR     1 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERT 185
               SCOP domains d3u04a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee...-------------.......eeeeeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u04 A   1 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEE-------------IEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERT 185
                                    10        20        30        40        50        60     |   -        80        90       100       110       120       130       140       150       160       170       180     
                                                                                            66            80
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U04)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q2GI30_EHRCR | Q2GI30)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042586    peptide deformylase activity    Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2GI30_EHRCR | Q2GI30: 3oca

(-) Related Entries Specified in the PDB File

3oca NATIVE STRUCTURE RELATED ID: EHCHA.01519.A RELATED DB: TARGETDB