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(-) Description

Title :  SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (GUANOSINE 5' -MONOPHOSPHATE) (ORTHORHOMBIC CRYSTAL FORM)
 
Authors :  L. Moynie, M. F. Giraud, A. Breton, F. Boissier, B. Daignan-Fornier, A. Dautant
Date :  02 Sep 08  (Deposition) - 17 Nov 09  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nucleus, Cytoplasm, Magnesium, Gmp Complex, Flip Peptide-Plane, Glycosyltransferase, Transferase, Metal-Binding, Purine Salvage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Moynie, M. F. Giraud, A. Breton, F. Boissier, B. Daignan-Fornier, A. Dautant
Functional Significance Of Four Successive Glycine Residues In The Pyrophosphate Binding Loop Of Fungal 6-Oxopurine Phosphoribosyltransferases.
Protein Sci. V. 21 1185 2012
PubMed-ID: 22610485  |  Reference-DOI: 10.1002/PRO.2098
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 2-221
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: Y1846
    Synonym: BYPASS OF REPRESSION BY ADENINE PROTEIN 6, HGPRTASE, HGPRT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
15GP4Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , GLU A:111 , ASP A:114 , THR A:115 , ARG A:116 , THR A:117 , THR A:118 , LYS A:159 , LYS A:187 , TRP A:188 , TYR A:189 , TYR A:191 , GLU A:194BINDING SITE FOR RESIDUE 5GP A 300
2AC2SOFTWAREGLY A:38 , GLY A:39 , ARG B:45 , ARG B:48BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREASP B:110 , GLU B:111 , ASP B:114 , THR B:115 , ARG B:116 , THR B:117 , THR B:118 , LYS B:159 , LYS B:187 , TRP B:188 , TYR B:189 , TYR B:191 , GLU B:194BINDING SITE FOR RESIDUE 5GP B 300
4AC4SOFTWAREARG A:45 , ARG A:48 , GLY B:38 , GLY B:39BINDING SITE FOR RESIDUE SO4 B 301
5AC5SOFTWAREASP C:110 , GLU C:111 , ASP C:114 , THR C:115 , ARG C:116 , THR C:117 , THR C:118 , LYS C:159 , LYS C:187 , TRP C:188 , TYR C:189 , TYR C:191 , GLU C:194BINDING SITE FOR RESIDUE 5GP C 300
6AC6SOFTWAREGLY C:38 , GLY C:39 , ARG D:45 , ARG D:48BINDING SITE FOR RESIDUE SO4 C 301
7AC7SOFTWAREASP D:110 , GLU D:111 , ASP D:114 , THR D:115 , ARG D:116 , THR D:117 , THR D:118 , LYS D:159 , LYS D:187 , TRP D:188 , TYR D:189 , TYR D:191 , GLU D:194BINDING SITE FOR RESIDUE 5GP D 300
8AC8SOFTWAREARG C:45 , ARG C:48 , GLY D:38 , GLY D:39BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JKZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JKZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JKZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JKZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2JKZ)

(-) 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:201
 aligned with HPRT_YEAST | Q04178 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
           HPRT_YEAST     5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh.......eeeeeeeeee..------------.eeeeee..hhhhhh......eeeee..ee..hhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee...................eeeee.....eeehhhhh.hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkz A   5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYED------------VKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
                                    14        24        34        44        54        64      |  -        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
                                                                                             71           84                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with HPRT_YEAST | Q04178 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
           HPRT_YEAST     5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh.......eeeeeeeeee..------------.eeeeee..hhhhhh......eeeee..ee..hhhhhhhhhhhhhhhhhhhhhh......hhhhh.eeeeeeeeeee.......hhhhhhh...eeeeeeee..eeehhhhh.hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkz B   5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYED------------VKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
                                    14        24        34        44        54        64      |  -        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
                                                                                             71           84                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:201
 aligned with HPRT_YEAST | Q04178 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
           HPRT_YEAST     5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh.......eeeeeeeeee..------------.eeeeee..hhhhhh......eeeee..ee..hhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee...................eeeee......eehhhhh.hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkz C   5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYED------------VKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
                                    14        24        34        44        54        64      |  -        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
                                                                                             71           84                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:201
 aligned with HPRT_YEAST | Q04178 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
           HPRT_YEAST     5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Pribosyltran-2jkzD01 D:5-137                                                                                                         -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Pribosyltran-2jkzD02 D:5-137                                                                                                         -------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) Pribosyltran-2jkzD03 D:5-137                                                                                                         -------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) Pribosyltran-2jkzD04 D:5-137                                                                                                         -------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh.......eeeeeeeeee..------------.eeeeee..hhhhhh......eeeee..ee..hhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeee.........hhhhh...eeeeeeee..eeehhhhh.hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkz D   5 DKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYED------------VKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQ 217
                                    14        24        34        44        54        64      |  -        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
                                                                                             71           84
   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 2JKZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JKZ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HPRT_YEAST | Q04178)
molecular function
    GO:0052657    guanine phosphoribosyltransferase activity    Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0004422    hypoxanthine phosphoribosyltransferase activity    Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0032263    GMP salvage    Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0032264    IMP salvage    Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    GO:0006178    guanine salvage    Any process that generates guanine, 2-amino-6-hydroxypurine, from derivatives of it without de novo synthesis.
    GO:0046100    hypoxanthine metabolic process    The chemical reactions and pathways involving hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPRT_YEAST | Q04178: 2jky 2xbu

(-) Related Entries Specified in the PDB File

2jky SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (GUANOSINE 5'-MONOPHOSPHATE) (TETRAGONAL CRYSTAL FORM)
2xbu SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (MONOCLINIC CRYSTAL FORM)