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(-) Description

Title :  HUMAN PHOSPHOSERINE AMINOTRANSFERASE IN COMPLEX WITH PLP
 
Authors :  L. Lehtio, T. Karlberg, J. Andersson, C. H. Arrowsmith, H. Berglund, C. R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Gras M. Hammarstrom, A. Johansson, I. Johansson, T. Kotenyova, M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman, K. Olesen, C. Persson, J. Sagemar S. G. Thorsell, L. Tresaugues, S. Van Den Berg, M. Welin, M. Wikstrom M. Wisniewska, J. Weigelt, H. Schueler, Structural Genomics Conso (Sgc)
Date :  18 Aug 08  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Phosphoserine Aminotransferase, Serc, Plp, Structural Genomics, Structural Genomics Consortium, Sgc, Amino-Acid Biosynthesis, Aminotransferase, Disease Mutation, Pyridoxal Phosphate, Serine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Lehtio, T. Karlberg, J. Andersson, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Kotenyova, M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman, K. Olesen C. Persson, J. Sagemark, S. G. Thorsell, L. Tresaugues, S. Van Den Berg, M. Welin, M. Wikstrom, M. Wisniewska, J. Weigelt, H. Schueler, Structural Genomics Consortium (Sgc)
Human Phosphoserine Aminotransferase In Complex With Plp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
    ChainsA, B, C
    EC Number2.6.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)GOLD PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 17 TO 370
    GenePSAT1, PSA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE, PSAT

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)AB 
Biological Unit 2 (2x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PLP-1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:78 , GLY A:79 , CYS A:80 , PHE A:83 , TRP A:107 , ASN A:154 , THR A:156 , ASP A:176 , SER A:178 , SER A:179 , GLN A:199 , LYS A:200 , HOH A:509 , HOH A:582 , ASN B:241 , THR B:242BINDING SITE FOR RESIDUE PLP A 400
2AC2SOFTWARELEU A:128 , GLY A:129 , SER A:130 , LYS A:133BINDING SITE FOR RESIDUE GOL A 500
3AC3SOFTWAREASN A:241 , THR A:242 , GLY B:78 , GLY B:79 , CYS B:80 , TRP B:107 , THR B:156 , ASP B:176 , SER B:178 , SER B:179 , GLN B:199 , LYS B:200 , HOH B:434BINDING SITE FOR RESIDUE PLP B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E77)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E77)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 12)

Asymmetric Unit (4, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048235P87ASERC_HUMANPolymorphism11540974A/B/CP87A
2UniProtVAR_072571A99VSERC_HUMANDisease (NLS2)587777778A/B/CA99V
3UniProtVAR_037252D100ASERC_HUMANDisease (PSATD)118203967A/B/CD100A
4UniProtVAR_072572S179LSERC_HUMANDisease (NLS2)587777777A/B/CS179L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048235P87ASERC_HUMANPolymorphism11540974A/BP87A
2UniProtVAR_072571A99VSERC_HUMANDisease (NLS2)587777778A/BA99V
3UniProtVAR_037252D100ASERC_HUMANDisease (PSATD)118203967A/BD100A
4UniProtVAR_072572S179LSERC_HUMANDisease (NLS2)587777777A/BS179L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048235P87ASERC_HUMANPolymorphism11540974CP87A
2UniProtVAR_072571A99VSERC_HUMANDisease (NLS2)587777778CA99V
3UniProtVAR_037252D100ASERC_HUMANDisease (PSATD)118203967CD100A
4UniProtVAR_072572S179LSERC_HUMANDisease (NLS2)587777777CS179L

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_HUMAN191-210
 
 
  3A:191-210
B:191-210
C:191-210
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_HUMAN191-210
 
 
  2A:191-210
B:191-210
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_HUMAN191-210
 
 
  2-
-
C:191-210

(-) Exons   (0, 0)

(no "Exon" information available for 3E77)

(-) 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:363
 aligned with SERC_HUMAN | Q9Y617 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:366
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364      
           SERC_HUMAN     5 RQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL 370
               SCOP domains d3e77a_    A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------3e77A01 A:20-260 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                             3e77A02 A:261-368 Aspartate Aminotransferase, domain 1                                                      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...---..hhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...eeee............hhhhh........eeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee...........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...hhhhh...eeeeee.....hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------A-----------VA------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e77 A   8 TENLYFQS---MLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL 370
                                   | - |      24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364      
                                  15  16                                                                                                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with SERC_HUMAN | Q9Y617 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:365
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365     
           SERC_HUMAN     6 QVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL 370
               SCOP domains d3e77b_    B: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------3e77B01 B:20-260 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                             3e77B02 B:261-368 Aspartate Aminotransferase, domain 1                                                      -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...---..hhhhhhhhhhhh.hhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.eeee............hhhhh.......eeeee.ee....ee...........eeee.hhhh.....hhhhh.eeeee..........eeeeee.hhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeeee.....hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------A-----------VA------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e77 B   9 ENLYFQS---MLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL 370
                                  |  -|       25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365     
                                 15  16                                                                                                                                                                                                                                                                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:362
 aligned with SERC_HUMAN | Q9Y617 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:365
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364     
           SERC_HUMAN     5 RQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQ 369
               SCOP domains d3e77c_    C: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------3e77C01 C:20-260 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                             3e77C02 C:261-368 Aspartate Aminotransferase, domain 1                                                      - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...---..hhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...eeee............hhhhh........eeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee...........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeeee.....hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------A-----------VA------------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e77 C   8 TENLYFQS---MLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQ 369
                                   | - |      24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364     
                                  15  16                                                                                                                                                                                                                                                                                                                                                                 

   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, 3)

Asymmetric Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E77)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SERC_HUMAN | Q9Y617)
molecular function
    GO:0004648    O-phospho-L-serine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0008615    pyridoxine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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