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(-) Description

Title :  MOLECULAR BASIS FOR THE LOCAL CONFOMATIONAL REARRANGEMENT OF HUMAN PHOSPHOSERINE PHOSPHATASE
 
Authors :  H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, K. Y. Hwang
Date :  21 Mar 02  (Deposition) - 01 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphatase, Conformational Rearrangement, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, E. Kim, D. Kwon, J. Yoon, D. Shin, E. J. Jeong, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, J. M. Cho, K. Y. Hwang
Molecular Basis For The Local Conformational Rearrangement Of Human Phosphoserine Phosphatase.
J. Biol. Chem. V. 277 46651 2002
PubMed-ID: 12213811  |  Reference-DOI: 10.1074/JBC.M204866200
(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 PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPSP, O-PHOSPHOSERINE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1APO2Ligand/IonD-2-AMINO-3-PHOSPHONO-PROPIONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , ASP A:22 , GLU A:29 , SER A:109 , GLY A:110 , LYS A:158 , ASP A:179 , GLY A:180 , THR A:182BINDING SITE FOR RESIDUE APO A 800
2AC2SOFTWAREASP B:20 , VAL B:21 , ASP B:22 , SER B:109 , GLY B:110 , LYS B:158 , THR B:182 , ASP B:183 , ARG B:202BINDING SITE FOR RESIDUE APO B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L8L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:7 -Arg A:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022378D32NSERB_HUMANDisease (PSPHD)28933976A/BD32N
2UniProtVAR_022379M52TSERB_HUMANDisease (PSPHD)104894036A/BM52T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L8L)

(-) Exons   (5, 10)

Asymmetric/Biological 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:4-47
B:4-47
44
44
1.7bENST000003954717bENSE00001018705chr7:56087427-56087293135SERB_HUMAN47-92462A:47-92
B:47-92
46
46
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:191-225
B:191-225
35
35

(-) Sequences/Alignments

Asymmetric/Biological 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:222
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           SERB_HUMAN     4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
               SCOP domains d1l8la_ A: Phosphoserine phosphatase                                                                                                                                                                                           SCOP domains
               CATH domains 1l8lA01                   1l8lA02 A:30-80,A:135-146                          1l8lA01 A:4-29,A:81-134,A:147-225                     1l8lA02     1l8lA01 A:4-29,A:81-134,A:147-225  [code=3.40.50.1000, no name defined]         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh.eeeee..........hhhhhhh..hhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......eeee.eeee....eeee...hhhhh..hhhhhhhhhhhhhh...eeeee.hhhhhh......eeeee.....hhhhhh....ee......hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------N-------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: A:4-47 UniProt: 1-47        --------------------------------------------Exon 1.8b  PDB: A:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: A:191-225          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.7b  PDB: A:47-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: A:141-190 UniProt: 141-190        ----------------------------------- Transcript 1 (2)
                 1l8l A   4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKFLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           SERB_HUMAN     4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
               SCOP domains d1l8lb_ B: Phosphoserine phosphatase                                                                                                                                                                                           SCOP domains
               CATH domains 1l8lB01                   1l8lB02 B:30-80,B:135-146                          1l8lB01 B:4-29,B:81-134,B:147-225                     1l8lB02     1l8lB01 B:4-29,B:81-134,B:147-225  [code=3.40.50.1000, no name defined]         CATH domains
           Pfam domains (1) ----------Hydrolase-1l8lB01 B:14-191                                                                                                                                                        ---------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Hydrolase-1l8lB02 B:14-191                                                                                                                                                        ---------------------------------- Pfam domains (2)
         Sec.struct. author ............eeee.........hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh......eeee..eee...........hhhhh..hhhhhhhhhhhhhh...eeee..hhhhhh......eee.......hhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------N-------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: B:4-47 UniProt: 1-47        --------------------------------------------Exon 1.8b  PDB: B:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: B:191-225          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.7b  PDB: B:47-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: B:141-190 UniProt: 141-190        ----------------------------------- Transcript 1 (2)
                 1l8l B   4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKFLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  

   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/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological 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 | P783301l8o 1nnl

(-) Related Entries Specified in the PDB File

1l8o 1L8O CONTATINS CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEX WITH PO4 AND SER