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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM T.ONNURINEUS IN COMPLEX WITH NDSB-201
 
Authors :  T. -Y. Jung, Y. -S. Kim, H. -N. Song, E. Woo
Date :  31 Mar 12  (Deposition) - 26 Dec 12  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  C,D  (4x)
Keywords :  Hydrolase, Haloacid Dehalogenase Superfamily, Ndsb (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
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector: PPROEX
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS ONNURINEUS
    Organism Taxid: 342948
    Other Details: ARAD139, GALE15, GALK16

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x): AB  
Biological Unit 2 (4x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 34)

Asymmetric Unit (2, 34)
No.NameCountTypeFull Name
11PS6Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 68)
No.NameCountTypeFull Name
11PS12Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2MSE56Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 68)
No.NameCountTypeFull Name
11PS12Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2MSE56Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:24 , ILE A:25 , THR A:26 , HOH A:2069 , ASN D:72BINDING SITE FOR RESIDUE 1PS A 201
2AC2SOFTWAREGLY A:38 , LEU A:39 , TRP A:45 , ASP A:133 , LYS A:134 , TYR A:153 , ALA A:154 , ASP A:155 , HOH A:2175 , HOH A:2232BINDING SITE FOR RESIDUE 1PS A 202
3AC3SOFTWAREGLY B:38 , LEU B:39 , TRP B:45 , ASP B:133 , LYS B:134 , TYR B:153 , HOH B:2142 , HOH B:2145 , HOH B:2148 , HOH B:2178BINDING SITE FOR RESIDUE 1PS B 202
4AC4SOFTWAREASN B:72 , ARG C:24 , ILE C:25 , THR C:26BINDING SITE FOR RESIDUE 1PS C 201
5AC5SOFTWAREGLY C:38 , TRP C:45 , ASP C:133 , LYS C:134 , TYR C:153 , ALA C:154 , ASP C:155 , HOH C:2174 , HOH C:2210BINDING SITE FOR RESIDUE 1PS C 202
6AC6SOFTWARELEU D:39 , TRP D:45 , ASP D:133 , LYS D:134 , TYR D:153 , HOH D:2142 , HOH D:2143 , HOH D:2161 , HOH D:2166BINDING SITE FOR RESIDUE 1PS D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AP9)

(-) Exons   (0, 0)

(no "Exon" information available for 4AP9)

(-) 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........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhhhh.eeeee........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap9 A  -6 GAmDPQFmKKVAVIDIEGTLTDFEFWREmARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFmANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAmGDGYADAKmFERADmGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                              |    | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143     | 153    |  163|      173       183       193
                              |    |                   22-MSE                                                                                    113-MSE                             149-MSE  158-MSE |                             
                             -4-MSE|                                                                                                                                                                164-MSE                         
                                   1-MSE                                                                                                                                                                                            


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 .eeehhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhh...eeeee........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap9 B  -6 GAmDPQFmKKVAVIDIEGTLTDFEFWREmARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFmANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAmGDGYADAKmFERADmGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                              |    | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143     | 153    |  163|      173       183       193
                             -4-MSE|                   22-MSE                                                                                    113-MSE                             149-MSE  158-MSE |                             
                                   1-MSE                                                                                                                                                            164-MSE                         


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...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhhhh.eeeee........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap9 C  -6 GAmDPQFmKKVAVIDIEGTLTDFEFWREmARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFmANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAmGDGYADAKmFERADmGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                              |    | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143     | 153    |  163|      173       183       193
                             -4-MSE|                   22-MSE                                                                                    113-MSE                             149-MSE  158-MSE |                             
                                   1-MSE                                                                                                                                                            164-MSE                         


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 .eeehhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeeeeeee...hhhhh....eeeeeeeeee..eeeeee....hhhhhhhhhh...eeeee....hhhhhhhh.eeeee........eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap9 D  -6 GAmDPQFmKKVAVIDIEGTLTDFEFWREmARITGKREIEELLEKGLSGEVEWLDSLLKRVGLIRGIDEGTFLRTREKVNVSPEARELVETLREKGFKVVLISGSFEEVLEPFKELGDEFmANRAIFEDGKFQGIRLRFRDKGEFLKRFRDGFILAmGDGYADAKmFERADmGIAVGREIPGADLLVKDLKELVDFIKNLK 193
                              |    | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143     | 153    |  163|      173       183       193
                             -4-MSE|                   22-MSE                                                                                    113-MSE                             149-MSE  158-MSE |                             
                                   1-MSE                                                                                                                                                            164-MSE
   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 4AP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AP9)

(-) 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: 4b6j

(-) Related Entries Specified in the PDB File

4b6j CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM T. ONNURINEUS