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(-) Description

Title :  CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCUS ELONGATUS
 
Authors :  D. Lorimer, J. Abendroth, T. Craig, A. Burgin, A. Segall, F. Rohwer
Date :  17 Feb 12  (Deposition) - 06 Mar 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
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 (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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FMT4Ligand/IonFORMIC ACID
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:66 , CYS A:109 , HIS A:151 , HIS A:155 , FMT A:203BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREGLN A:183 , ALA A:184 , ARG A:186 , HOH A:382 , GLN D:183 , ALA D:184 , ARG D:186BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWAREGLY A:61 , GLN A:66 , CYS A:109 , LEU A:110 , HIS A:151 , GLU A:152 , HIS A:155 , ZN A:201BINDING SITE FOR RESIDUE FMT A 203
04AC4SOFTWARECYS B:109 , HIS B:151 , HIS B:155 , FMT B:204BINDING SITE FOR RESIDUE ZN B 201
05AC5SOFTWAREALA B:10 , GLN B:52 , HOH B:490BINDING SITE FOR RESIDUE CL B 202
06AC6SOFTWAREGLN A:106 , TYR A:116 , HOH A:446 , LYS B:34 , ARG B:35BINDING SITE FOR RESIDUE EDO B 203
07AC7SOFTWAREGLY B:61 , GLN B:66 , CYS B:109 , LEU B:110 , HIS B:151 , GLU B:152 , HIS B:155 , ZN B:201 , HOH B:459BINDING SITE FOR RESIDUE FMT B 204
08AC8SOFTWARECYS C:109 , HIS C:151 , HIS C:155 , FMT C:203BINDING SITE FOR RESIDUE ZN C 201
09AC9SOFTWAREGLN B:183 , ALA B:184 , ARG B:186 , HOH B:320 , GLN C:183 , ALA C:184 , ARG C:186 , HOH C:334BINDING SITE FOR RESIDUE EDO C 202
10BC1SOFTWAREGLY C:61 , GLN C:66 , CYS C:109 , LEU C:110 , HIS C:151 , GLU C:152 , HIS C:155 , ZN C:201BINDING SITE FOR RESIDUE FMT C 203
11BC2SOFTWAREGLN D:66 , CYS D:109 , HIS D:151 , HIS D:155 , FMT D:202BINDING SITE FOR RESIDUE ZN D 201
12BC3SOFTWAREGLY D:61 , GLN D:66 , CYS D:109 , LEU D:110 , HIS D:151 , GLU D:152 , HIS D:155 , ZN D:201 , HOH D:493BINDING SITE FOR RESIDUE FMT D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DR8)

(-) Exons   (0, 0)

(no "Exon" information available for 4DR8)

(-) 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:188
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
         A0A0H3JZJ4_S     2 TAAVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPVA 189
               SCOP domains d4dr8a_ 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
                 4dr8 A   2 TAAVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPVA 189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
         A0A0H3JZJ4_S     4 AVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPVAA 190
               SCOP domains d4dr8b_ 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
                 4dr8 B   4 AVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPVAA 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
         A0A0H3JZJ4_S     4 AVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
               SCOP domains d4dr8c_ 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
                 4dr8 C   4 AVAIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     


Chain D from PDB  Type:PROTEIN  Length:183
 aligned with A0A0H3JZJ4_S | A0A0H3JZJ4 from UniProtKB/TrEMBL  Length:192

    Alignment length:183
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   
         A0A0H3JZJ4_S     6 AIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
               SCOP domains d4dr8d_ 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
                 4dr8 D   6 AIRVAKKKLAKPPLDLHYLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHLNGVLFVDRVENRLELNEALDKKGFAVQAVRPV 188
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185
   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 4DR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DR8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DR8)

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        A0A0H3JZJ4_S | A0A0H3JZJ4: 4dr9

(-) Related Entries Specified in the PDB File

3uwa 3uwb 4dr9