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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Kamo, N. Kudo, W. C. Lee, K. Ito, H. Motoshim, M. Tanokura, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 Nov 03  (Deposition) - 28 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Peptide Deformylase, Protein Synthesis, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kamo, N. Kudo, W. C. Lee, K. Ito, H. Motoshim, M. Tanokura
The Crystal Structure Of Peptide Deformylase From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(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
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3) PLYS S
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1V3Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1V3Y)

(-) 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:170
 aligned with DEF_THETH | P43522 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
            DEF_THETH     1 MVYPIRLYGDPVLRRKARPVEDFSGIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVEYADEPEGEEERPLRELVRRVYVVANPVITYREGLVEGTEGCLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRAELVRFQKEA 182
               SCOP domains d1v3ya_ A: Peptide deformylase                                                                                                                                                         SCOP domains
               CATH domains 1v3yA00 A:1-182 Peptide Deformylase                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.........hhhhhhhhhhhhhhhh...eee.hhhh....eeeee.------------.......eeeeeeeeeeeee..eeeee.........eeeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3y A   1 MVYPIRLYGDPVLRRKARPVEDFSGIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVE------------LRELVRRVYVVANPVITYREGLVEGTEGcLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRAELVRFQKEA 182
                                    10        20        30        40        50        60|        -   |    80        90       100 |     110       120       130       140       150       160       170       180  
                                                                                       61           74                         102-OCS                                                                            


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with DEF_THETH | P43522 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
            DEF_THETH     2 VYPIRLYGDPVLRRKARPVEDFSGIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVEYADEPEGEEERPLRELVRRVYVVANPVITYREGLVEGTEGCLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRAELVRFQKEAR 183
               SCOP domains d1v3yb_ B: Peptide deformylase                                                                                                                                                         SCOP domains
               CATH domains 1v3yB00 B:2-183 Peptide Deformylase                                                                                                                                                    CATH domains
           Pfam domains (1) Pep_deformylase-1v3yB01 B:2-165                                                                                                                                     ------------------ Pfam domains (1)
           Pfam domains (2) Pep_deformylase-1v3yB02 B:2-165                                                                                                                                     ------------------ Pfam domains (2)
         Sec.struct. author ........hhhhhh.........hhhhhhhhhhhhhhhh...eee.hhhh....eeeeee.---------------..eeeeeeeeeeeeee..eeeee.........eeeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3y B   2 VYPIRLYGDPVLRRKARPVEDFSGIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVEY---------------VRRVYVVANPVITYREGLVEGTEGcLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRAELVRFQKEAR 183
                                    11        21        31        41        51        61|        -      | 81        91       101|      111       121       131       141       151       161       171       181  
                                                                                       62              78                     102-OCS
   Legend:   → Mismatch (orange background)
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  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  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEF_THETH | P43522)
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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