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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI PEPTIDE DEFORMYLASE
 
Authors :  J. Cai
Date :  02 Nov 05  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Cobalt Hicobacter Pylori Peptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Cai, C. Han, T. Hu, J. Zhang, D. Wu, F. Wang, Y. Liu, J. Ding, K. Chen, J. Yue, X. Shen, H. Jiang
Peptide Deformylase Is A Potential Target For Anti-Helicobacter Pylori Drugs: Reverse Docking, Enzymatic Assay, And X-Ray Crystallography Validation
Protein Sci. V. 15 2071 2006
PubMed-ID: 16882991  |  Reference-DOI: 10.1110/PS.062238406
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:96 , HIS A:138 , HIS A:142 , HOH A:368BINDING SITE FOR RESIDUE CO A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EW7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:9 -Pro A:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EW7)

(-) Exons   (0, 0)

(no "Exon" information available for 2EW7)

(-) 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:163
 aligned with Q2L8P7_HELPX | Q2L8P7 from UniProtKB/TrEMBL  Length:174

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
         Q2L8P7_HELPX     2 ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKEL 164
               SCOP domains d2ew7a_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2ew7A00 A:2-164 Peptide Deformylase                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........hhhhheeeeeeeeeeee..eeeee.........eeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ew7 A   2 ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKEL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   


Chain A from PDB  Type:PROTEIN  Length:163
 aligned with Q672W7_HELPX | Q672W7 from UniProtKB/TrEMBL  Length:174

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
         Q672W7_HELPX     2 ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKEL 164
               SCOP domains d2ew7a_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2ew7A00 A:2-164 Peptide Deformylase                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........hhhhheeeeeeeeeeee..eeeee.........eeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ew7 A   2 ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKEL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EW7)

(-) Gene Ontology  (5, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q672W7_HELPX | Q672W7)
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.

Chain A   (Q2L8P7_HELPX | Q2L8P7)
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
        Q672W7_HELPX | Q672W7: 2ew5 2ew6 4e9a 4e9b

(-) Related Entries Specified in the PDB File

2ew5 HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR
2ew6 HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR