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(-) Description

Title :  PEPTIDE DEFORMYLASE (NI-FORM) WITH HYDROSULFIDE
 
Authors :  G. J. Palm, W. Hinrichs
Date :  29 Feb 12  (Deposition) - 04 Apr 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Oxidation-Reduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Strianese, G. J. Palm, S. Milione, O. Kuehl, W. Hinrichs, C. Pellecchia
A Fret Enzyme-Based Probe For Monitoring Hydrogen Sulfide.
Inorg. Chem. V. 51 11220 2012
PubMed-ID: 23072298  |  Reference-DOI: 10.1021/IC301363D

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B, C
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B PLUS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Other Details: C-TERMINAL HIS TAG
    Strain: BL21(DE3)
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1H2S3Ligand/IonHYDROSULFURIC ACID
2NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1H2S1Ligand/IonHYDROSULFURIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1H2S1Ligand/IonHYDROSULFURIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1H2S1Ligand/IonHYDROSULFURIC ACID
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:50 , CYS A:90 , HIS A:132 , HIS A:136 , H2S A:1002BINDING SITE FOR RESIDUE NI A1001
2AC2SOFTWAREGLY A:45 , GLN A:50 , GLU A:133 , NI A:1001BINDING SITE FOR RESIDUE H2S A1002
3AC3SOFTWAREGLN B:50 , CYS B:90 , HIS B:132 , HIS B:136 , H2S B:1002BINDING SITE FOR RESIDUE NI B1001
4AC4SOFTWAREGLY B:45 , GLN B:50 , LEU B:91 , GLU B:133 , NI B:1001BINDING SITE FOR RESIDUE H2S B1002
5AC5SOFTWAREGLN C:50 , CYS C:90 , HIS C:132 , HIS C:136 , H2S C:1002BINDING SITE FOR RESIDUE NI C1001
6AC6SOFTWAREGLY C:45 , GLN C:50 , GLU C:133 , NI C:1001BINDING SITE FOR RESIDUE H2S C1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AL2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:8 -Pro A:9
2Ile B:8 -Pro B:9
3Ile C:8 -Pro C:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AL2)

(-) Exons   (0, 0)

(no "Exon" information available for 4AL2)

(-) 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:162
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLD 163
               SCOP domains d4al2a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....eee.......eee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4al2 A   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLD 162
                                    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 DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKAR 168
               SCOP domains d4al2b_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....ee.........ee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4al2 B   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKAR 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       


Chain C from PDB  Type:PROTEIN  Length:162
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLD 163
               SCOP domains d4al2c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....ee.........ee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4al2 C   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLD 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AL2)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DEF_ECOLI | P0A6K3)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_ECOLI | P0A6K3: 1bs4 1bs5 1bs6 1bs7 1bs8 1bsj 1bsk 1bsz 1def 1dff 1dtf 1g27 1g2a 1icj 1lru 1xem 1xen 1xeo 2ai8 2def 2dtf 2kmn 2w3t 2w3u 3k6l 4al3 4az4 4v5b

(-) Related Entries Specified in the PDB File

1bs4 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL
1bs5 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM
1bs6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER
1bs7 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM
1bs8 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER
1bsj COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI
1bsk ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI
1bsz PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL
1def PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1 - 147), NMR, 9 STRUCTURES
1dff PEPTIDE DEFORMYLASE
1dtf PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1
1g27 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASECOMPLEXED WITH THE INHIBITOR BB-3497
1g2a THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASECOMPLEXED WITH ACTINONIN
1icj PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)
1lru CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXEDWITH ANTIBIOTIC ACTINONIN
1xem HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ZINC-PEPTIDE DEFORMYLASE BOUND TO FORMATE
1xen HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI IRON-PEPTIDE DEFORMYLASE BOUND TO FORMATE
1xeo HIGH RESOLUTION CRYSTALS STRUCTURE OF COBALT- PEPTIDEDEFORMYLASE BOUND TO FORMATE
2ai8 E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH SB-485343
2def PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1 - 147), NMR, 20 STRUCTURES
2dtf PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1
2vhm STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME
2w3t CHLORO COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE
2w3u FORMATE COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE
4al3 PEPTIDE DEFORMYLASE (CO-FORM) WITH MERCAPTOETHANOL