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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHOSERINE PHOSPHATASE
 
Authors :  Y. Peeraer, A. Rabijns, C. Verboven, J. F. Collet, E. Van Schaftingen, C. De Ranter
Date :  14 Jan 03  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphoserine Phosphatase, Psp, Hpsp, Phospho-Aspartyl, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Peeraer, A. Rabijns, C. Verboven, J. F. Collet, E. Van Schaftingen, C. De Ranter
High-Resolution Structure Of Human Phosphoserine Phosphatase In Open Conformation.
Acta Crystallogr. , Sect. D V. 59 971 2003
PubMed-ID: 12777757  |  Reference-DOI: 10.1107/S0907444903005407
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-3-PHOSPHOSERINE PHOSPHATASE
    ChainsA, B
    EC Number3.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET7A
    Expression System StrainBL21(DE3)-PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOSERINE PHOSPHATASE

 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  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL6Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:110 , LYS A:158 , HOH A:1028BINDING SITE FOR RESIDUE CL A 1500
2AC2SOFTWAREPHE B:112 , SER B:114 , LEU B:135 , HOH B:1053BINDING SITE FOR RESIDUE CL B 1502
3AC3SOFTWARESER A:114 , LEU A:135BINDING SITE FOR RESIDUE CL A 1503
4AC4SOFTWAREGLY A:30 , GLY A:111 , PHE A:112 , ILE A:115BINDING SITE FOR RESIDUE CL A 1505
5AC5SOFTWAREGLY B:30 , GLY B:111 , PHE B:112 , HOH B:1072BINDING SITE FOR RESIDUE CL B 1506
6AC6SOFTWAREGLY B:110 , LYS B:158 , HOH B:1068 , HOH B:1183BINDING SITE FOR RESIDUE CL B 1507
7AC7SOFTWAREASP A:20 , ASP A:22 , ASP A:179 , HOH A:1026 , HOH A:1028 , HOH A:1069BINDING SITE FOR RESIDUE CA A 2001
8AC8SOFTWAREASP B:20 , ASP B:22 , ASP B:179 , HOH B:1021 , HOH B:1068 , HOH B:1117BINDING SITE FOR RESIDUE CA B 2002
9AC9SOFTWAREGLU B:185 , PRO B:188 , HOH B:1137 , HOH B:1222 , HOH B:1223 , HOH B:1401BINDING SITE FOR RESIDUE CA B 2003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Cys A:187 -Pro A:188
2Pro A:188 -Pro A:189
3Cys B:187 -Pro B:188
4Pro B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022378D32NSERB_HUMANDisease (PSPHD)28933976A/BD32N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022378D32NSERB_HUMANDisease (PSPHD)28933976AD32N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022378D32NSERB_HUMANDisease (PSPHD)28933976BD32N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003954711aENSE00001749046chr7:56119297-56118831467SERB_HUMAN-00--
1.3dENST000003954713dENSE00001638092chr7:56101847-56101654194SERB_HUMAN-00--
1.5aENST000003954715aENSE00001337387chr7:56099747-56099622126SERB_HUMAN-00--
1.6cENST000003954716cENSE00002171169chr7:56088924-56088766159SERB_HUMAN1-47472A:5-44
B:5-46
40
42
1.7bENST000003954717bENSE00001018705chr7:56087427-56087293135SERB_HUMAN47-92462A:57-92
B:57-92
36
36
1.8bENST000003954718bENSE00001121162chr7:56085072-56084927146SERB_HUMAN92-141502A:92-141
B:92-141
50
50
1.9bENST000003954719bENSE00000976989chr7:56082864-56082716149SERB_HUMAN141-190502A:141-190
B:141-190
50
50
1.10cENST0000039547110cENSE00001521802chr7:56079562-56078761802SERB_HUMAN191-225352A:191-221
B:191-221
31
31

(-) 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:205
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:217
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
           SERB_HUMAN     5 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG 221
               SCOP domains d1nnla_ A: Phosphoserine phosphatase                                                                                                                                                                                      SCOP domains
               CATH domains 1nnlA01                  1nnlA02 A:30-80            ,A:135-146              1nnlA01 A:5-29,A:81-134,A:147-221                     1nnlA02     1nnlA01 A:5-29,A:81-134,A:147-221  [code=3.40.50.1000, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeee........hhhhhhhhhh......------------hhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh..hhh.eeee.eee.....eeee...hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhh......eeeee.....hhhhhhhh.eee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: A:5-44 UniProt: 1-47       --------------------------------------------Exon 1.8b  PDB: A:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: A:191-221      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.7b  PDB: A:57-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: A:141-190 UniProt: 141-190        ------------------------------- Transcript 1 (2)
                 1nnl A   5 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAV------------PFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG 221
                                    14        24        34        44         -  |     64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
                                                                  44           57                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:217
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
           SERB_HUMAN     5 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG 221
               SCOP domains d1nnlb_ B: Phosphoserine phosphatase                                                                                                                                                                                      SCOP domains
               CATH domains 1nnlB01                  1nnlB02 B:30-80,B          :135-146                1nnlB01 B:5-29,B:81-134,B:147-221                     1nnlB02     1nnlB01 B:5-29,B:81-134,B:147-221  [code=3.40.50.1000, no name defined]     CATH domains
           Pfam domains (1) ---------Hydrolase-1nnlB01 B:14-191                                                                                                                                                        ------------------------------ Pfam domains (1)
           Pfam domains (2) ---------Hydrolase-1nnlB02 B:14-191                                                                                                                                                        ------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhh.....eeeee........hhhhhhhhhh........----------hhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh..hhh.eeee.eee.....eeee...hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhh.....eeeee.....hhhhhh....ee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: B:5-46 UniProt: 1-47       --------------------------------------------Exon 1.8b  PDB: B:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: B:191-221      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.7b  PDB: B:57-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: B:141-190 UniProt: 141-190        ------------------------------- Transcript 1 (2)
                 1nnl B   5 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSE----------PFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG 221
                                    14        24        34        44 |       -  |     64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
                                                                    46         57                                                                                                                                                                    

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SERB_HUMAN | P78330)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0006563    L-serine metabolic process    The chemical reactions and pathways involving 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.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SERB_HUMAN | P783301l8l 1l8o

(-) Related Entries Specified in the PDB File

1f5s CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE FROM METHANOCOCCUS JANNASCHII
1j97 PHOSPHO-ASPARTYL INTERMEDIATE ANALOGUE OF PHOSPHOSERINE PHOSPHATASE
1l7m HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX)
1l7n TRANSITION STATE ANALOGUE OF PHOSPHOSERINE PHOSPHATASE (ALUMINUM FLUORIDE COMPLEX)
1l7o CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE IN APO FORM
1l7p SUBSTRATE BOUND PHOSPHOSERINE PHOSPHATASE COMPLEX STRUCTURE