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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM LEPTOSPIRA INTERROGANS (LIPDF) AT PH7.0
 
Authors :  Z. Zhou, X. Song, Y. Li, W. Gong
Date :  06 Apr 04  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Closed Conformation, Hepes, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhou, X. Song, W. Gong
Novel Conformational States Of Peptide Deformylase From Pathogenic Bacterium Leptospira Interrogans: Implications For Population Shift
J. Biol. Chem. V. 280 42391 2005
PubMed-ID: 16239225  |  Reference-DOI: 10.1074/JBC.M506370200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: LEPTOSPIRA INTERROGANS
    Organism Taxid: 173
    Synonym: LIPDF, PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:53 , CYS A:101 , HIS A:143 , HIS A:147 , HOH A:1717BINDING SITE FOR RESIDUE ZN A 1513
2AC2SOFTWARECYS B:101 , HIS B:143 , HIS B:147 , HOH B:2718BINDING SITE FOR RESIDUE ZN B 2514
3AC3SOFTWAREGLY A:46 , VAL A:47 , GLY A:48 , ARG A:70 , TYR A:71 , PHE A:97 , TRP A:98 , GLU A:99 , GLY A:100 , CYS A:101 , LEU A:102 , TYR A:136 , GLU A:144 , HOH A:1717BINDING SITE FOR RESIDUE EPE A 1716
4AC4SOFTWAREGLY B:46 , VAL B:47 , GLY B:48 , TYR B:71 , PHE B:97 , GLU B:99 , GLY B:100 , CYS B:101 , LEU B:102 , TYR B:136 , HIS B:143 , GLU B:144 , HOH B:2718BINDING SITE FOR RESIDUE EPE B 2717

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VEY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VEY)

(-) 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:171
 aligned with DEF_LEPIN | Q93LE9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
            DEF_LEPIN     2 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDS 172
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1veyA00 A:1-171 Peptide Deformylase                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eee.hhhh....eeee................eeee...eee....eeeeeeee..eeeeeeeeeee.eeee...........eeeehhhhhhhhhhhhhhhh.hhhhh......eeehhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vey A   1 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDS 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with DEF_LEPIN | Q93LE9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
            DEF_LEPIN     2 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDS 172
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1veyB00 B:1-171 Peptide Deformylase                                                                                                                                         CATH domains
           Pfam domains (1) -Pep_deformylase-1veyB01 B:2-163                                                                                                                                   -------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1veyB02 B:2-163                                                                                                                                   -------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.................eee....ee....eeeee........ee.eeeee.eeee...........eeeehhhhhhhhhhhhhhhh.hhhhhh......eehhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vey B   1 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDS 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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  (0, 0)

(no "SCOP Domain" information available for 1VEY)

(-) 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_LEPIN | Q93LE9)
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_LEPIN | Q93LE9: 1sv2 1szz 1vev 1vez 1y6h

(-) Related Entries Specified in the PDB File

1rn5 LIPDF AT PH3.0
1sv2 LIPDF AT PH7.5
1vev LIPDF AT PH6.5
1vez LIPDF AT PH8.0