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(-) Description

Title :  PEPTIDE DEFORMYLASE FROM VIBRIO CHOLERAE
 
Authors :  J. Osipiuk, R. Mulligan, L. Papazisi, W. F. Anderson, A. Joachimiak, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  23 Feb 11  (Deposition) - 09 Mar 11  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Peptide Deformylase, Metal Binding, Hydrolase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, R. Mulligan, L. Papazisi, W. F. Anderson, A. Joachimiak
Peptide Deformylase From Vibrio Cholerae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 2
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF, DEF2, VC_A0150
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: O1 BIOVAR ELTOR STR. N16961
    Synonym: PDF 2, POLYPEPTIDE DEFORMYLASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
3ZN7Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:51 , CYS A:91 , HIS A:133 , HIS A:137 , HOH A:219 , ZN A:505BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWARETYR A:98 , HOH A:217 , ZN A:507 , ASP B:96 , HIS B:162BINDING SITE FOR RESIDUE ZN B 502
03AC3SOFTWAREASP A:96 , HIS A:162 , ZN A:507 , TYR B:98 , HOH B:215BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREGLN B:51 , CYS B:91 , HIS B:133 , HIS B:137 , HOH B:223 , ZN B:506BINDING SITE FOR RESIDUE ZN B 504
05AC5SOFTWAREGLY A:46 , GLU A:134 , HOH A:219 , ZN A:501 , ARG B:168BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWAREARG A:168 , GLY B:46 , GLU B:134 , HOH B:223 , HOH B:318 , ZN B:504BINDING SITE FOR RESIDUE ZN B 506
07AC7SOFTWAREASP A:96 , HOH A:217 , HOH A:257 , ZN A:503 , ASP B:96 , HOH B:215 , HOH B:216 , ZN B:502BINDING SITE FOR RESIDUE ZN A 507
08AC8SOFTWAREPRO A:10 , ASP A:11 , ARG A:15 , HOH A:231BINDING SITE FOR RESIDUE CL A 508
09AC9SOFTWAREPRO B:10 , ASP B:11 , ARG B:15 , HOH B:308BINDING SITE FOR RESIDUE CL B 509
10BC1SOFTWAREARG A:13 , GLY A:53 , THR B:8 , PRO B:10 , ASP B:11 , HOH B:230 , HOH B:268 , HOH B:269 , HOH B:306BINDING SITE FOR RESIDUE SO4 B 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QU1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:9 -Pro A:10
2Ala B:9 -Pro B:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QU1)

(-) Exons   (0, 0)

(no "Exon" information available for 3QU1)

(-) 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:168
 aligned with DEF2_VIBCH | Q9KN16 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
           DEF2_VIBCH     1 MAVLEILTAPDPRLRVQSKQVTDVASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQPLVLINPKVVSGSNKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKNRAR 168
               SCOP domains d3qu1a_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh......hhhhhhhhhhhhhhhhhhh....eee.hhhh....eeee.........eeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qu1 A   1 MAVLEILTAPDPRLRVQSKQVTDVASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQPLVLINPKVVSGSNKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKNRAR 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with DEF2_VIBCH | Q9KN16 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           DEF2_VIBCH     2 AVLEILTAPDPRLRVQSKQVTDVASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQPLVLINPKVVSGSNKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKNRAR 168
               SCOP domains d3qu1b_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Pep_deformylase-3qu1B01 B:3-153                                                                                                                        --------------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-3qu1B02 B:3-153                                                                                                                        --------------- Pfam domains (2)
         Sec.struct. author .........hhhhh.......hhhhhhhhhhhhhhhhhhh....eee.hhhh....eeee.........eeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu1 B   2 AVLEILTAPDPRLRVQSKQVTDVASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQPLVLINPKVVSGSNKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKNRAR 168
                                    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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QU1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pep_deformylase] (48)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEF2_VIBCH | Q9KN16)
molecular function
    GO:0008463    formylmethionine deformylase activity    Catalysis of the reaction: N-formyl-L-methionine + H(2)O = L-methionine + formate.
    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:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0043686    co-translational protein modification    The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
    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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