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(-) Description

Title :  PHOSPHO-ASPARTYL INTERMEDIATE ANALOGUE OF PHOSPHOSERINE PHOSPHATASE
 
Authors :  H. Cho, W. Wang, R. Kim, H. Yokota, S. Damo, S. -H. Kim, D. Wemmer, S. Kustu, D. Yan, Berkeley Structural Genomics Center (Bsgc)
Date :  24 May 01  (Deposition) - 25 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphoserine Phosphatase, Psp, Phospho-Aspartyl, Beryllium Fluoride, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Cho, W. Wang, R. Kim, H. Yokota, S. Damo, S. -H. Kim, D. Wemmer, S. Kustu, D. Yan
Bef(3)(-) Acts As A Phosphate Analog In Proteins Phosphorylated On Aspartate: Structure Of A Bef(3)(-) Complex With Phosphoserine Phosphatase.
Proc. Natl. Acad. Sci. Usa V. 98 8525 2001
PubMed-ID: 11438683  |  Reference-DOI: 10.1073/PNAS.131213698
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)/PSJS1244
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1BFD2Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREBFD A:11 , ASP A:13 , ASP A:167 , HOH A:808 , HOH A:828BINDING SITE FOR RESIDUE MG A 220
2AC2SOFTWAREBFD B:511 , ASP B:513 , ASP B:667 , HOH B:809 , HOH B:821BINDING SITE FOR RESIDUE MG B 720
3AC3SOFTWAREASN B:607 , LYS B:610 , GLU B:611 , LYS B:691 , CYS B:697 , GLU B:699 , HOH B:901 , HOH B:1057BINDING SITE FOR RESIDUE PO4 B 230
4AC4SOFTWARELYS A:4 , ASN B:548 , GLU B:550 , HOH B:804 , HOH B:832 , HOH B:928BINDING SITE FOR RESIDUE PO4 B 240

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J97)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J97)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J97)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J97)

(-) Exons   (0, 0)

(no "Exon" information available for 1J97)

(-) 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:210
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           SERB_METJA     2 EKKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1j97a_ A: Phosphoserine phosphatase                                                                                                                                                                               SCOP domains
               CATH domains 1j97A01        1j97A02 A:17-77 Phosphoserine phosphatase; domain 2          1j97A01 A:2-16,A:78-210  [code=3.40.50.1000, no name defined]                                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.........hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j97 A   2 EKKKKLILFdFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
                                    11-BFD                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202         
           SERB_METJA     3 KKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1j97b_ B: Phosphoserine phosphatase                                                                                                                                                                              SCOP domains
               CATH domains 1j97B01       1j97B02 B:517-577 Phosphoserine phosphatase; domain 2        1j97B01 B:503-516,B:578-710  [code=3.40.50.1000, no name defined]                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j97 B 503 KKKKLILFdFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 711
                                   512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702         
                                  511-BFD
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J97)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SERB_METJA | Q58989)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SERB_METJA | Q58989: 1f5s 1l7m 1l7n 1l7o 1l7p

(-) Related Entries Specified in the PDB File

1f5s 1F5S IS THE CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM METHANOCOCCUS JANNASCHII RELATED ID: BSGCAIR30380 RELATED DB: TARGETDB