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(-) Description

Title :  ASYMETRIC GTP BOUND STRUCTURE OF UPRTASE FROM SULFOLOBUS SOLFATARICUS CONTAINING PRPP-MG2+ IN HALF OF THE ACTIVE SITES AND R5P AND PPI IN THE OTHER HALF
 
Authors :  A. Kadziola, S. Christoffersen
Date :  09 Feb 09  (Deposition) - 01 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Allosteric Regulation, Tetramer, Sulfolobus Solfataricus, Phosphoribosyltransferase, Prpp, R5P, Gtp, Pop, Magnesium, Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Christoffersen, A. Kadziola, E. Johansson, M. Rasmussen, M. Willemoes, K. F. Jensen
Structural And Kinetic Studies Of The Allosteric Transition In Sulfolobus Solfataricus Uracil Phosphoribosyltransferase: Permanent Activation By Engineering Of The C-Terminus
J. Mol. Biol. V. 393 464 2009
PubMed-ID: 19683539  |  Reference-DOI: 10.1016/J.JMB.2009.08.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLFS2
    Expression System Strain: NF1830
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSO0231, UPP
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: UMP PYROPHOSPHORYLASE, UPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2HSX3Ligand/Ion5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3MG4Ligand/IonMAGNESIUM ION
4POP2Ligand/IonPYROPHOSPHATE 2-
5PRP2Ligand/IonALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:30 , ARG A:34 , ARG A:37 , HOH A:219 , HOH A:229 , MG A:302 , ARG B:37 , LYS B:91 , PRO B:94 , ASN D:27 , LYS D:30 , ARG D:34 , GTP D:217BINDING SITE FOR RESIDUE GTP A 301
02AC2SOFTWAREHOH A:219 , HOH A:229 , GTP A:301 , GTP D:217BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREARG A:80 , ALA A:81 , ARG A:105 , MET A:117 , ASP A:140 , MET A:142 , ALA A:144 , THR A:145 , ALA A:146 , SER A:147 , THR A:148 , GLY A:211 , HOH A:217 , HOH A:218 , HOH A:223 , MG A:305BINDING SITE FOR RESIDUE PRP A 303
04AC4SOFTWARELEU A:79 , ARG A:80 , HOH A:217 , HOH A:218 , PRP A:303BINDING SITE FOR RESIDUE MG A 305
05AC5SOFTWARELYS A:91 , PRO A:94 , LYS B:30 , ARG B:34 , ARG B:37 , HOH B:218 , MG B:302 , ILE C:26 , ASN C:27 , LYS C:30 , ARG C:34 , HOH D:218 , GTP D:301BINDING SITE FOR RESIDUE GTP B 301
06AC6SOFTWAREHOH B:218 , GTP B:301 , HOH D:218 , GTP D:301BINDING SITE FOR RESIDUE MG B 302
07AC7SOFTWAREARG B:105 , ASP B:140 , MET B:142 , ALA B:144 , THR B:145 , ALA B:146 , SER B:147 , THR B:148 , HOH B:220 , POP B:307BINDING SITE FOR RESIDUE HSX B 306
08AC8SOFTWARELEU B:79 , ARG B:80 , ALA B:81 , GLY B:211 , HSX B:306 , TYR D:123BINDING SITE FOR RESIDUE POP B 307
09AC9SOFTWAREARG C:105 , ASP C:140 , MET C:142 , ALA C:144 , THR C:145 , ALA C:146 , SER C:147 , THR C:148 , POP C:307BINDING SITE FOR RESIDUE HSX C 306
10BC1SOFTWARETYR A:123 , LYS A:125 , LEU C:79 , ARG C:80 , ALA C:103 , HSX C:306BINDING SITE FOR RESIDUE POP C 307
11BC2SOFTWAREILE B:26 , ASN B:27 , LYS B:30 , ARG B:34 , HOH B:218 , GTP B:301 , MG B:302 , LYS C:30 , ARG C:34 , ARG D:37 , LYS D:91 , PRO D:94 , HOH D:218 , HOH D:225BINDING SITE FOR RESIDUE GTP D 301
12BC3SOFTWAREILE A:26 , ASN A:27 , LYS A:30 , ARG A:34 , HOH A:219 , HOH A:220 , HOH A:229 , GTP A:301 , MG A:302 , ARG C:37 , LYS C:91 , PRO C:94 , LYS D:30 , ARG D:34BINDING SITE FOR RESIDUE GTP D 217
13BC4SOFTWARELEU D:79 , ARG D:80 , ALA D:81 , SER D:104 , ARG D:105 , ASP D:140 , ILE D:143 , ALA D:144 , THR D:145 , ALA D:146 , SER D:147 , THR D:148 , HOH D:219 , HOH D:220 , HOH D:224 , MG D:304 , HSX D:306BINDING SITE FOR RESIDUE PRP D 303
14BC5SOFTWAREGLU D:107 , TYR D:202 , GLY D:208 , ASP D:209 , PRP D:303BINDING SITE FOR RESIDUE HSX D 306
15BC6SOFTWARELEU D:79 , ARG D:80 , ALA D:81 , HOH D:219 , HOH D:220 , PRP D:303BINDING SITE FOR RESIDUE MG D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G6W)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:204 -Pro A:205
2Leu B:204 -Pro B:205
3Leu C:204 -Pro C:205
4Leu D:204 -Pro D:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G6W)

(-) Exons   (0, 0)

(no "Exon" information available for 3G6W)

(-) 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:215
 aligned with UPP_SULSO | Q980Q4 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            UPP_SULSO     2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
               SCOP domains d3g6wa_ A: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 3g6wA00 A:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eee...hhhhh.eeeeee..hhhhhhhhhhh....eeeeeeeee...............eeeeee.........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6w A   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with UPP_SULSO | Q980Q4 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            UPP_SULSO     2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
               SCOP domains d3g6wb_ B: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 3g6wB00 B:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeeehhhhh.eeeeee..hhhhhhhhhh......eeeeeeee.---------.....eeeeee.........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6w B   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASR---------KDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101   |     -   |   121       131       141       151       161       171       181       191       201       211     
                                                                                                                                 105       115                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:207
 aligned with UPP_SULSO | Q980Q4 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            UPP_SULSO     2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
               SCOP domains d3g6wc_ C: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 3g6wC00 C:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeeeehhhhh.eeeeee..hhhhhhhhhh......eeeeeeee..--------.....eeeeee.........eeeee..ee..hhhhhhhhhhhhhhh..eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6w C   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRV--------KDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101    |    -   |   121       131       141       151       161       171       181       191       201       211     
                                                                                                                                  106      115                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:215
 aligned with UPP_SULSO | Q980Q4 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            UPP_SULSO     2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
               SCOP domains d3g6wd_ D: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 3g6wD00 D:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeehhhhh.eeeeee..hhhhhhhhhh......eeeeeeeee.............eeeeeee.........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eeehhhhhhhhh.....eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6w D   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G6W)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (UPP_SULSO | Q980Q4)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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).
    GO:0004845    uracil phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
    GO:0044206    UMP salvage    Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
    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:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
    GO:0008655    pyrimidine-containing compound salvage    Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
    GO:0006223    uracil salvage    Any process that generates uracil, 2,4-dioxopyrimidine, from derivatives of it without de novo synthesis.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  3g6w
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  UPP_SULSO | Q980Q4
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 Related Entries

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

UniProtKB/Swiss-Prot
        UPP_SULSO | Q980Q4: 1vst 1xtt 1xtu 1xtv

(-) Related Entries Specified in the PDB File

1vst
1xtt SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE (UMP)
1xtu SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE (UMP) AND CYTIDINE 5' -TRIPHOSPHATE (CTP)
1xtv SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE WITH URIDINE 5'-MONOPHOSPHATE (UMP) BOUND TO HALF OF THE SUBUNITS