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(-) Description

Title :  SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE (UMP)
 
Authors :  S. Arent, P. Harris, K. F. Jensen, S. Larsen
Date :  24 Oct 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetramer, Type 1 Phosphoribosyltransferase, Ump Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Arent, P. Harris, K. F. Jensen, S. Larsen
Allosteric Regulation And Communication Between Subunits In Uracil Phosphoribosyltransferase From Sulfolobus Solfataricus(, )
Biochemistry V. 44 883 2005
PubMed-ID: 15654744  |  Reference-DOI: 10.1021/BI048041L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE URACIL PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUHE23-2
    Expression System Strain: NF1830
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 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  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2U5P4Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ASP A:140 , MET A:142 , ALA A:144 , THR A:145 , ALA A:146 , SER A:147 , THR A:148 , GLY A:201 , TYR A:202 , ILE A:203 , GLY A:208 , ASP A:209 , ALA A:210 , HOH A:1251 , HOH A:1252 , HOH A:1265 , HOH A:1277 , HOH A:1289BINDING SITE FOR RESIDUE U5P A 1250
2AC2SOFTWAREARG B:80 , ASP B:140 , MET B:142 , ALA B:144 , THR B:145 , ALA B:146 , SER B:147 , THR B:148 , GLY B:201 , TYR B:202 , ILE B:203 , GLY B:208 , ASP B:209 , ALA B:210 , HOH B:2254 , HOH B:2256 , HOH B:2263 , HOH B:2280 , HOH B:2306BINDING SITE FOR RESIDUE U5P B 2250
3AC3SOFTWAREARG C:105 , ASP C:140 , MET C:142 , ALA C:144 , THR C:145 , ALA C:146 , SER C:147 , THR C:148 , GLY C:201 , TYR C:202 , ILE C:203 , GLY C:208 , ASP C:209 , ALA C:210 , HOH C:3251 , HOH C:3253 , HOH C:3257 , HOH C:3262BINDING SITE FOR RESIDUE U5P C 3250
4AC4SOFTWAREARG D:80 , ARG D:105 , ASP D:140 , MET D:142 , ALA D:144 , THR D:145 , ALA D:146 , SER D:147 , THR D:148 , GLY D:201 , TYR D:202 , ILE D:203 , GLY D:208 , ASP D:209 , ALA D:210 , HOH D:4254 , HOH D:4266 , HOH D:4269 , HOH D:4276 , HOH D:4318BINDING SITE FOR RESIDUE U5P D 4250
5AC5SOFTWAREASN B:77 , ILE B:78 , LEU B:79 , ARG B:80 , ALA B:81 , ALA B:82 , VAL B:83 , PHE B:215 , TYR C:123BINDING SITE FOR RESIDUE ACY B 2252
6AC6SOFTWARETYR A:123 , ASN D:77 , ILE D:78 , LEU D:79 , ARG D:80 , ALA D:81 , ALA D:82 , VAL D:83 , PHE D:215BINDING SITE FOR RESIDUE ACY D 4252

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:79 -Arg A:80
2Leu A:204 -Pro A:205
3Leu B:204 -Pro B:205
4Leu C:79 -Arg C:80
5Leu C:204 -Pro C:205
6Leu D:204 -Pro D:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XTT)

(-) 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 d1xtta1 A:2-216 Uracil PRTase, Upp                                                                                                                                                                                      SCOP domains
               CATH domains 1xttA00 A:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeehhhhh.eeeeeee..hhhhhhhhhhhh...eeeeeeeee.............eeeeeee.........eeeee..ee..hhhhhhhhhhhhhhh..eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtt 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:208
 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 d1xttb_ B: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 1xttB00 B: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...hhhhhhhhhhhh...eeeeeeeee.-------.....eeeeeee.........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtt B   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRV-------PKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101    |    -  |    121       131       141       151       161       171       181       191       201       211     
                                                                                                                                  106     114                                                                                                      


Chain C 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 d1xttc_ C: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 1xttC00 C:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeehhhhh.eeeeeee..hhhhhhhhhhhh...eeeeeeeee.............eeeeeee.........eeeee..ee..hhhhhhhhhhhhhhh..eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtt C   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 D from PDB  Type:PROTEIN  Length:208
 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 d1xttd_ D: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 1xttD00 D:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
           Pfam domains (1) -----------------------------------------------------------Pribosyltran-1xttD01 D:61-170                                                                                 ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------Pribosyltran-1xttD02 D:61-170                                                                                 ---------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------Pribosyltran-1xttD03 D:61-170                                                                                 ---------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------Pribosyltran-1xttD04 D:61-170                                                                                 ---------------------------------------------- Pfam domains (4)
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeehhhhh.eeeeee...hhhhhhhhhhhh...eeeeeeeee.-------.....eeeeeee.........eeeee..ee..hhhhhhhhhhhhhh...eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xtt D   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRV-------PKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101    |    -  |    121       131       141       151       161       171       181       191       201       211     
                                                                                                                                  106     114
   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, 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  (1, 4)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        UPP_SULSO | Q980Q4: 1vst 1xtu 1xtv 3g6w

(-) Related Entries Specified in the PDB File

1xtu THE SAME PROTEIN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE, CYTIDINE 5'-TRIPHOSPHATE
1xtv THE SAME PROTEIN WITH URIDINE 5'-MONOPHOSPHATE BOUND TO HALF OF THE SUBUNITS