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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) LYASE DDDK COMPLEXED WITH NICKEL AND DIACRYLATE
 
Authors :  N. J. Schnicker, M. Dey
Date :  27 Sep 16  (Deposition) - 14 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dmsp Lyase, Cupin, Nickel Dependent, Metal Binding, Oxidoreductase (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, B
    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 A HIS-TAG.
    Strain: HTCC1062

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
17BC2Ligand/Ion3-(ACRYLOYLOXY)PROPANOIC ACID
2NI2Ligand/IonNICKEL (II) ION
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , HIS A:58 , GLU A:62 , HIS A:96 , 7BC A:202binding site for residue NI A 201
2AC2SOFTWAREVAL A:24 , TRP A:26 , LEU A:53 , HIS A:56 , HIS A:58 , GLU A:62 , TYR A:64 , HIS A:96 , TYR A:122 , NI A:201binding site for residue 7BC A 202
3AC3SOFTWAREARG B:-3 , GLY B:-2 , SER B:-1 , TYR B:122 , PHE B:123 , PRO B:124 , HOH B:310binding site for residue PEG B 201
4AC4SOFTWAREASP A:33 , PHE A:34 , GLY B:102 , LYS B:103 , HOH B:323 , HOH B:331binding site for residue PEG B 202
5AC5SOFTWAREVAL A:65 , VAL A:66 , LYS A:84 , GLY A:85 , THR B:67 , LYS B:84 , TYR B:109binding site for residue PEG B 203
6AC6SOFTWAREHIS B:56 , HIS B:58 , GLU B:62 , HIS B:96 , 7BC B:205binding site for residue NI B 204
7AC7SOFTWARETYR B:21 , TRP B:26 , LEU B:53 , HIS B:56 , HIS B:58 , GLU B:62 , TYR B:64 , HIS B:96 , TYR B:122 , NI B:204binding site for residue 7BC B 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhh............eeeeeeehhhhhh....eeeeeee....eeeeee....eeeeeee.eeeeee..eeeeee...eeee.....eeee......eeeeeee...hhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tfz A   0 HMIFVKNLASVLSQEWSSTEKYPGVRWKFLIDADFDGSSGLSLGFAEIAPGGDLTLHYHSPAEIYVVTNGKGILNKSGKLETIKKGDVVYIAGNAEHALKNNGKETLEFYWIFPTDRFSEVEYFPAK 126
                                     9        19        29        39        49        59        69        79        89        99       109       119       


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeehhhhhh....ee......eeeeeeehhhhhh....eeeeeee....eeeeee....eeeeeee.eeeeee..eeeeee...eeee.....eeee......eeeeeee...hhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tfz B  -4 PRGSHMIFVKNLASVLSQEWSSTEKYPGVRWKFLIDADFDGSSGLSLGFAEIAPGGDLTLHYHSPAEIYVVTNGKGILNKSGKLETIKKGDVVYIAGNAEHALKNNGKETLEFYWIFPTDRFSEVEYFPAK 126
                                     5        15        25        35        45        55        65        75        85        95       105       115       125
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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UniProtKB/Swiss-Prot
        Q4FNM4_PELUB | Q4FNM4: 5tg0

(-) Related Entries Specified in the PDB File

5tg0