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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin, J. Vincent, I. Warner, C. Ericson, S. A. Lesley
Date :  06 Nov 02  (Deposition) - 24 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metalloenzyme, Drug Design, Deformylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin J. Vincent, I. Warner, C. Ericson, S. A. Lesley
Structure Analysis Of Peptide Deformylases From Streptococcus Pneumoniae, Staphylococcus Aureus, Thermotoga Maritima, And Pseudomonas Aeruginosa: Snapshots Of The Oxygen Sensitivity Of Peptide Deformylase
J. Mol. Biol. V. 330 309 2003
PubMed-ID: 12823970  |  Reference-DOI: 10.1016/S0022-2836(03)00596-5

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH4
    Expression System Strain: GENEHOGS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:92 , HIS A:134 , HIS A:138 , HOH A:402BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREGLN B:51 , CYS B:92 , HIS B:134 , HIS B:138 , HOH B:403BINDING SITE FOR RESIDUE ZN B 402
3AC3SOFTWARETYR A:88 , GLU A:90 , GLY A:91 , CYS A:131 , HIS A:134 , GOL A:303 , HOH A:528BINDING SITE FOR RESIDUE GOL A 301
4AC4SOFTWAREGLU B:90 , GLY B:91 , CYS B:131 , GLU B:135 , HOH B:473 , HOH B:511 , HOH B:517BINDING SITE FOR RESIDUE GOL B 302
5AC5SOFTWAREGLY A:44 , ILE A:45 , GLY A:46 , GLY A:91 , CYS A:92 , LEU A:93 , GOL A:301BINDING SITE FOR RESIDUE GOL A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N5N)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:9 -Pro A:10
2Ala A:42 -Pro A:43
3Phe B:9 -Pro B:10
4Ala B:42 -Pro B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N5N)

(-) Exons   (0, 0)

(no "Exon" information available for 1N5N)

(-) 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:167
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
            DEF_PSEAE     1 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQ 167
               SCOP domains d1n5na_ A: Peptide deformylase                                                                                                                                          SCOP domains
               CATH domains 1n5nA00 A:1-167 Peptide Deformylase                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee....eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n5n A   1 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQ 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_PSEAE     2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHR 165
               SCOP domains d1n5nb_ B: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1n5nB00 B:2-165 Peptide Deformylase                                                                                                                                  CATH domains
           Pfam domains (1) -Pep_deformylase-1n5nB01 B:3-154                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1n5nB02 B:3-154                                                                                                                         ----------- Pfam domains (2)
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee........ee.........ee.....eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n5n B   2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHR 165
                                    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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEF_PSEAE | Q9I7A8)
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:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_PSEAE | Q9I7A8: 1ix1 1lry 1s17

(-) Related Entries Specified in the PDB File

1lm4 PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCUS AUREUS
1lm6 PEPTIDE DEFORMYLASE FROM STREPTOCOCCUS PNEUMONIAE
1lme PEPTIDE DEFORMYLASE FROM THERMOTOGA MARITIMA