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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE 2 WITH ACTINONIN FROM BACILLUS CEREUS
 
Authors :  E. E. Kim
Date :  17 Jan 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Park, K. H. Kim, J. H. Moon, E. E. Kim
Characterization Of Peptide Deformylase2 From B. Cereus
J. Biochem. Mol. Biol. V. 40 1050 2007
PubMed-ID: 18047803

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 2
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF2
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579
    Synonym: PDF 2, POLYPEPTIDE DEFORMYLASE 2

 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BB24Ligand/IonACTINONIN
2CIT1Ligand/IonCITRIC ACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2CIT1Ligand/IonCITRIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2CIT-1Ligand/IonCITRIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CYS A:110 , HIS A:153 , HIS A:157 , BB2 A:401BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREGLN B:65 , CYS B:110 , HIS B:153 , HIS B:157 , BB2 B:403BINDING SITE FOR RESIDUE ZN B 602
3AC3SOFTWAREARG A:56 , PRO A:57 , GLY A:58 , ILE A:59 , GLY A:60 , GLN A:65 , LEU A:104 , GLY A:107 , GLU A:108 , GLY A:109 , CYS A:110 , LEU A:111 , ILE A:149 , HIS A:153 , GLU A:154 , HIS A:157 , ZN A:601 , HOH A:632 , BB2 B:402 , HOH B:754BINDING SITE FOR RESIDUE BB2 A 401
4AC4SOFTWAREGLN A:45 , PRO A:57 , BB2 A:401 , BB2 A:404 , HOH A:683 , GLN B:105 , LEU B:182 , ARG B:184 , HOH B:610 , HOH B:611 , HOH B:629 , HOH B:646 , HOH B:654 , HOH B:688BINDING SITE FOR RESIDUE BB2 B 402
5AC5SOFTWAREBB2 A:404 , HOH A:724 , ARG B:56 , PRO B:57 , GLY B:58 , ILE B:59 , GLY B:60 , GLN B:65 , LEU B:104 , GLY B:107 , GLU B:108 , GLY B:109 , CYS B:110 , LEU B:111 , HIS B:153 , GLU B:154 , HIS B:157 , ZN B:602 , HOH B:654BINDING SITE FOR RESIDUE BB2 B 403
6AC6SOFTWAREGLN A:105 , LEU A:182 , ARG A:184 , HOH A:627 , HOH A:632 , HOH A:633 , HOH A:642 , HOH A:690 , HOH A:745 , GLN B:45 , PRO B:57 , BB2 B:402 , BB2 B:403BINDING SITE FOR RESIDUE BB2 A 404
7AC7SOFTWARETHR A:128 , ARG A:142 , HOH A:630 , HOH A:665 , ILE B:95 , THR B:128 , LYS B:140 , ARG B:142BINDING SITE FOR RESIDUE CIT A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OKL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:24 -Pro A:25
2Leu B:24 -Pro B:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OKL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OKL)

(-) Exons   (0, 0)

(no "Exon" information available for 2OKL)

(-) 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:185
 aligned with DEF2_BACCR | Q819K2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:185
                             1                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     
           DEF2_BACCR     - -MLTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGLAAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKPLER 184
               SCOP domains d2okla_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2oklA00 A:0-184 Peptide Deformylase                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeeee.....eeeeeeeeeeeeee...eee...................ee.eeeeeeee....eeeeeeehhhhhhhhhhhhhhh..hhhhhh...........eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okl A   0 HMLTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGLAAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKPLER 184
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with DEF2_BACCR | Q819K2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
           DEF2_BACCR     1 MLTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGLAAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKPLER 184
               SCOP domains d2oklb_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains 2oklB00 B:1-184 Peptide Deformylase                                                                                                                                                      CATH domains
           Pfam domains (1) ---Pep_deformylase-2oklB01 B:4-173                                                                                                                                           ----------- Pfam domains (1)
           Pfam domains (2) ---Pep_deformylase-2oklB02 B:4-173                                                                                                                                           ----------- Pfam domains (2)
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeeee.....eeeeeeeeeeeeee...eee...................ee.eeeeeeee....eeeeeeehhhhhhhhhhhhhhh..hhhhhh...........eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okl B   1 MLTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGLAAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKPLER 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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   (DEF2_BACCR | Q819K2)
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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1ws0 STRUCTURE ANALYSIS OF PEPTIDE DEFORMYLASE FROM BACILLUS CEREUS
1ws1 STRUCTURE ANALYSIS OF PEPTIDE DEFORMYLASE WITH ACTINONIN FROM BACILLUS CEREUS