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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) LYASE DDDK COMPLEXED WITH IRON AND ZINC
 
Authors :  N. J. Schnicker, M. Dey
Date :  27 Sep 16  (Deposition) - 14 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dmsp Lyase, Cupin, Nickel Dependent, Metal Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Schnicker, S. M. De Silva, J. D. Todd, M. Dey
Structural And Biochemical Insights Into Dimethylsulfoniopropionate Cleavage By Cofactor-Bound Dddk From The Prolific Marine Bacterium Pelagibacter.
Biochemistry V. 56 2873 2017
PubMed-ID: 28511016  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00099

(-) Compounds

Molecule 1 - DIMETHYLSULFONIOPROPIONATE LYASE DDDK
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SAR11_0394
    Organism Scientific: PELAGIBACTER UBIQUE (STRAIN HTCC1062)
    Organism Taxid: 335992
    Other Details: RESIDUES 1-20 IN THE SEQUENCE ARE FROM THE VECTOR FOR THE HIS TAG.
    Strain: HTCC1062

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , HIS A:58 , GLU A:62 , TYR A:64 , HIS A:96 , ZN A:202 , HOH A:321binding site for residue FE A 201
2AC2SOFTWAREHIS A:56 , HIS A:58 , GLU A:62 , TYR A:64 , HIS A:96 , FE A:201 , HOH A:321binding site for residue ZN A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TG0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TG0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TG0)

(-) Exons   (0, 0)

(no "Exon" information available for 5TG0)

(-) Sequences/Alignments

Asymmetric Unit
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Chain A from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....hhhhh............eeeeeee..........eeeeeee....eeeeeee...eeeeeee.eeeeee..eeeeee...eeee.....eeee......eeeeeee...hhhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tg0 A  -6 LVPRGSHMIFVKNLASVLSQEWSSTEKYPGVRWKFLIDADFDGSSGLSLGFAEIAPGGDLTLHYHSPAEIYVVTNGKGILNKSGKLETIKKGDVVYIAGNAEHALKNNGKETLEFYWIFPTDRFSEVEYFPAKQKSG 130
                                     3        13        23        33        43        53        63        73        83        93       103       113       123
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5TG0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TG0)

(-) Gene Ontology  (0, 0)

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 Related Entries

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        Q4FNM4_PELUB | Q4FNM4: 5tfz

(-) Related Entries Specified in the PDB File

5tfz