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(-) Description

Title :  CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCUS ELONGATUS IN COMPLEX WITH ACTINONIN
 
Authors :  D. Lorimer, J. Abendroth, T. Craig, A. Burgin, A. Segall, F. Rohwler
Date :  17 Feb 12  (Deposition) - 16 Jan 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Frank, D. Lorimer, M. Youle, P. Witte, T. Craig, J. Abendroth, F. Rohwer, R. A. Edwards, A. M. Segall, A. B. Burgin
Structure And Function Of A Cyanophage-Encoded Peptide Deformylase.
Isme J V. 7 1150 2013
PubMed-ID: 23407310  |  Reference-DOI: 10.1038/ISMEJ.2013.4

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B, C, D
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: VCID 6622
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF, SYC0213_D, YP_170923
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 269084
    Strain: PCC6301
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1BB24Ligand/IonACTINONIN
2BR5Ligand/IonBROMIDE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2BR-1Ligand/IonBROMIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2BR-1Ligand/IonBROMIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2BR-1Ligand/IonBROMIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2BR-1Ligand/IonBROMIDE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:66 , CYS A:109 , HIS A:151 , HIS A:155 , BB2 A:203BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREARG A:186 , BR D:202BINDING SITE FOR RESIDUE BR A 202
03AC3SOFTWAREGLY A:59 , ILE A:60 , GLY A:61 , GLN A:66 , GLU A:107 , GLY A:108 , CYS A:109 , LEU A:110 , HIS A:151 , GLU A:152 , HIS A:155 , ZN A:201 , HOH A:350 , HOH A:355 , ARG B:35BINDING SITE FOR RESIDUE BB2 A 203
04AC4SOFTWAREGLN B:66 , CYS B:109 , HIS B:151 , HIS B:155 , BB2 B:203BINDING SITE FOR RESIDUE ZN B 201
05AC5SOFTWAREALA B:184 , ARG B:186 , HOH B:356 , BR C:203BINDING SITE FOR RESIDUE BR B 202
06AC6SOFTWARESER A:37 , GLY B:59 , ILE B:60 , GLY B:61 , GLN B:66 , GLY B:108 , CYS B:109 , LEU B:110 , HIS B:151 , GLU B:152 , HIS B:155 , ZN B:201 , HOH B:430BINDING SITE FOR RESIDUE BB2 B 203
07AC7SOFTWAREGLN C:66 , CYS C:109 , HIS C:151 , HIS C:155 , BB2 C:204BINDING SITE FOR RESIDUE ZN C 201
08AC8SOFTWARESER C:37 , LYS C:71BINDING SITE FOR RESIDUE BR C 202
09AC9SOFTWAREBR B:202 , ALA C:184 , ARG C:186BINDING SITE FOR RESIDUE BR C 203
10BC1SOFTWAREGLY C:59 , ILE C:60 , GLY C:61 , GLN C:66 , GLU C:107 , GLY C:108 , CYS C:109 , LEU C:110 , TYR C:116 , ARG C:147 , HIS C:151 , GLU C:152 , HIS C:155 , ZN C:201 , ARG D:35BINDING SITE FOR RESIDUE BB2 C 204
11BC2SOFTWAREGLN D:66 , CYS D:109 , HIS D:151 , HIS D:155 , BB2 D:203BINDING SITE FOR RESIDUE ZN D 201
12BC3SOFTWAREALA A:184 , BR A:202 , ALA D:184 , ARG D:186 , HOH D:413BINDING SITE FOR RESIDUE BR D 202
13BC4SOFTWAREGLY D:59 , ILE D:60 , GLY D:61 , GLN D:66 , GLN D:106 , GLY D:108 , CYS D:109 , LEU D:110 , TYR D:116 , HIS D:151 , GLU D:152 , HIS D:155 , ZN D:201BINDING SITE FOR RESIDUE BB2 D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DR9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4DR9)

(-) 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:182
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
         A0A0H3JZJ4_S     2 TAAVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
               SCOP domains d4dr9a_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee....-----..eeeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dr9 A   2 TAAVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLEL-----PPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
                                    11        21        31        41        51        61        71        |-    |   91       101       111       121       131       141       151       161       171       181       
                                                                                                         80    86                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:182
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  
         A0A0H3JZJ4_S     6 AIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRP 187
               SCOP domains d4dr9b_ B: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee...........eeeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dr9 B   6 AIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRP 187
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  


Chain C from PDB  Type:PROTEIN  Length:184
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
         A0A0H3JZJ4_S     5 VAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
               SCOP domains d4dr9c_ C: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee...........eeeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dr9 C   5 VAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
         A0A0H3JZJ4_S     5 VAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
               SCOP domains d4dr9d_ D: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee...........eeeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dr9 D   5 VAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DR9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DR9)

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        A0A0H3JZJ4_S | A0A0H3JZJ4: 4dr8

(-) Related Entries Specified in the PDB File

3uwa 3uwb 4dr8