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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYL DIPHOSPHATE SYNTHASE FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  A. Kadziola, E. Johansson, C. H. Jepsen, J. Mcguire, S. Larsen, B. Hove- Jensen
Date :  11 Aug 04  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Prpp Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kadziola, C. H. Jepsen, E. Johansson, J. Mcguire, S. Larsen, B. Hove-Jensen
Novel Class Iii Phosphoribosyl Diphosphate Synthase: Structure And Properties Of The Tetrameric, Phosphate-Activated, Non-Allosterically Inhibited Enzyme From Methanocaldococcus Jannaschii
J. Mol. Biol. V. 354 815 2005
PubMed-ID: 16288921  |  Reference-DOI: 10.1016/J.JMB.2005.10.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
    Chains: A, B, C, D
    EC Number: 2.7.6.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PHOSPHORIBOSYL DIPHOSPHATE SYNTHASE
    Gene: PRS
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: PHOSPHORIBOSYL DIPHOSPHATE SYNTHASE;
RPPK

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1U9Y)

(-) Sites  (0, 0)

(no "Site" information available for 1U9Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U9Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1U9Y)

(-) 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:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9ya1 A:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9ya2 A:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9yA01 A:1-141,A:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9yA02 A:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9yA01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh..eee..----------............eeeeeee...hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh..eeeee.......eee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9y A   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9yb1 B:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9yb2 B:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9yB01 B:1-141,B:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9yB02 B:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9yB01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh..eee..----------..........eeeeeeeee...hhhhhhhhhhhhhh.eeeeeeeeee.....hhhhhhhhhh..eeeee.......eee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9y B   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9yc1 C:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9yc2 C:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9yC01 C:1-141,C:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9yC02 C:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9yC01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh..eee..----------..........eeeeeeeee...hhhhhhhhhhhhhh.eeeeeeeeee.....hhhhhhhhhh..eeeee.......eee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9y C   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        


Chain D from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9yd1 D:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9yd2 D:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9yD01 D:1-141,D:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9yD02 D:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9yD01   CATH domains
           Pfam domains (1) Pribosyltran_N-1u9yD05 D:1-115                                                                                     -----------------Pribosyltran-1u9yD01 D:133-242                                                                                ------------------------------------------ Pfam domains (1)
           Pfam domains (2) Pribosyltran_N-1u9yD06 D:1-115                                                                                     -----------------Pribosyltran-1u9yD02 D:133-242                                                                                ------------------------------------------ Pfam domains (2)
           Pfam domains (3) Pribosyltran_N-1u9yD07 D:1-115                                                                                     -----------------Pribosyltran-1u9yD03 D:133-242                                                                                ------------------------------------------ Pfam domains (3)
           Pfam domains (4) Pribosyltran_N-1u9yD08 D:1-115                                                                                     -----------------Pribosyltran-1u9yD04 D:133-242                                                                                ------------------------------------------ Pfam domains (4)
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh.eeee..----------..........eeeeeeeee...hhhhhhhhhhhhhh.eeeeeeeeee.....hhhhhhhhhh..eeeee.......eee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9y D   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196
   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, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: [code=3.40.50.2020, no name defined] (117)
(-)
Methanocaldococcus jannaschii. Organism_taxid: 2190. (2)
1a1u9yA01A:1-141,A:276-284
1b1u9yB01B:1-141,B:276-284
1c1u9yC02C:142-275
1d1u9yD02D:142-275
1e1u9yC01C:1-141,C:276-284
1f1u9yD01D:1-141,D:276-284
1g1u9yA02A:142-275
1h1u9yB02B:142-275

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: PRTase-like (59)
(-)
Clan: no clan defined [family: Pribosyltran_N] (7)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KPRS_METJA | Q58761)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004749    ribose phosphate diphosphokinase activity    Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+).
    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:0006015    5-phosphoribose 1-diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
    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:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
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

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        KPRS_METJA | Q58761: 1u9z

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1u9z