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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM T. ONNURINEUS
 
Authors :  T. -Y. Jung, Y. -S. Kim, H. -N. Song, E. Woo
Date :  14 Aug 12  (Deposition) - 26 Dec 12  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.34
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Hydrolase, L-Serine, Haloacid Dehalogenase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. -Y. Jung, Y. S-Kim, B. H. Oh, E. Woo
Identification Of A Novel Ligand Binding Site In Phosphoserine Phosphatase From The Hyperthermophilic Archaeon Thermococcus Onnurineus.
Proteins V. 81 819 2013
PubMed-ID: 23239422  |  Reference-DOI: 10.1002/PROT.24238

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI MC1061
    Expression System Taxid: 1211845
    Expression System Variant: ARAD139, GALE15, GALK16
    Expression System Vector: PPROEX
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS ONNURINEUS NA1
    Organism Taxid: 523850

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4B6J)

(-) Sites  (0, 0)

(no "Site" information available for 4B6J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B6J)

(-) Exons   (0, 0)

(no "Exon" information available for 4B6J)

(-) 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:200
 aligned with B6YX36_THEON | B6YX36 from UniProtKB/TrEMBL  Length:194

    Alignment length:200
                                   1                                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         B6YX36_THEON     - -------MKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhh.eeeee........hhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhh....eeeeeeeeee..eeeeeee...hhhhhhhhhh...eeeee....hhhhhh...eeeee........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6j A  -6 GAMDPQFMKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with B6YX36_THEON | B6YX36 from UniProtKB/TrEMBL  Length:194

    Alignment length:200
                                   1                                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         B6YX36_THEON     - -------MKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhh...eeeee........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6j B  -6 GAMDPQFMKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with B6YX36_THEON | B6YX36 from UniProtKB/TrEMBL  Length:194

    Alignment length:200
                                   1                                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         B6YX36_THEON     - -------MKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhhhh..eeeeeeeeee..eeeeeee...hhhhhhhhhh...eeeee....hhhhhh...eeeee........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6j C  -6 GAMDPQFMKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with B6YX36_THEON | B6YX36 from UniProtKB/TrEMBL  Length:194

    Alignment length:200
                                   1                                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
         B6YX36_THEON     - -------MKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhheeeeee........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeeeeee...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhh...eeeee........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6j D  -6 GAMDPQFMKKVAVIDIEGTLTDFEFWREMARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAMGDGYADAKMFERADMGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
   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  (0, 0)

(no "SCOP Domain" information available for 4B6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B6J)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B6YX36_THEON | B6YX36)
molecular function
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        B6YX36_THEON | B6YX36: 4ap9

(-) Related Entries Specified in the PDB File

4ap9 CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM T. ONNURINEUS IN COMPLEX WITH NDSB-201