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(-) Description

Title :  STRUCTURE OF AQ2163 PROTEIN FROM AQUIFEX AEOLICUS
 
Authors :  N. K. Lokanath, Riken Structural Genomics/Proteomics Initiative
Date :  19 Dec 06  (Deposition) - 01 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Uracil Phosphoribosyl Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Kamiya, K. J. Pampa, N. Kunishima
Structure Of Aq2163 Protein From Aquifex Aeolicus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: UMP PYROPHOSPHORYLASE, UPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:102 , ALA A:132 , THR A:133 , GLY A:134 , GLY A:135 , THR A:136 , HOH A:1314BINDING SITE FOR RESIDUE SO4 A 1301
2AC2SOFTWAREARG B:102 , SER B:109 , ALA B:132 , THR B:133 , GLY B:134 , GLY B:135 , THR B:136 , HOH B:1395BINDING SITE FOR RESIDUE SO4 B 1302
3AC3SOFTWAREARG C:102 , ALA C:132 , THR C:133 , GLY C:134 , GLY C:135 , THR C:136 , HOH C:1315 , HOH C:1377 , HOH C:1398BINDING SITE FOR RESIDUE SO4 C 1303
4AC4SOFTWAREARG D:102 , ALA D:132 , THR D:133 , GLY D:134 , GLY D:135 , THR D:136 , HOH D:1328 , HOH D:1329 , HOH D:1376 , HOH D:1385BINDING SITE FOR RESIDUE SO4 D 1304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E55)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:76 -Arg A:77
2Ile A:192 -Pro A:193
3Leu B:76 -Arg B:77
4Ile B:192 -Pro B:193
5Leu C:76 -Arg C:77
6Ile C:192 -Pro C:193
7Leu D:76 -Arg D:77
8Ile D:192 -Pro D:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E55)

(-) Exons   (0, 0)

(no "Exon" information available for 2E55)

(-) 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:208
 aligned with UPP_AQUAE | O67914 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            UPP_AQUAE     1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
               SCOP domains d2e55a_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2e55A00 A:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.hhh.eeeeeee..hhhhhhhhhhhh...ee.eeeeee......eeeeeee.......eeeee..ee..hhhhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e55 A   1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with UPP_AQUAE | O67914 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            UPP_AQUAE     1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
               SCOP domains d2e55b_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2e55B00 B:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.hhh.eeeeeee..hhhhhhhhhhhh...ee.eeeeee......eeeeeee.......eeeee..ee..hhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e55 B   1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with UPP_AQUAE | O67914 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            UPP_AQUAE     1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
               SCOP domains d2e55c_ C: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2e55C00 C:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.hhh.eeeeeee..hhhhhhhhhhhh...ee.eeeeee......eeeeeee.......eeeee..ee..hhhhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e55 C   1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain D from PDB  Type:PROTEIN  Length:208
 aligned with UPP_AQUAE | O67914 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            UPP_AQUAE     1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
               SCOP domains d2e55d_ D: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2e55D00 D:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.hhh.eeeeeee..hhhhhhhhhhhh...ee.eeeeee......eeeeeee.......eeeee..ee..hhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e55 D   1 MIVELSHPLIKHKVNTARIQDTSAEKLRKTLKELGFMLVYEALKDILLEEKEVRTWIGNKRFNYLNEEEIVFVPILRAGLSFLEGALQVVPNAKVGFLGIKRNEETLESHIYYSRLPELKGKIVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFKEVEIFVGNVDERLNDKGYIIPGLGDIGDRLYAVSVY 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (0, 0)

(no "Pfam Domain" information available for 2E55)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (UPP_AQUAE | O67914)
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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  2e55
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 Related Entries

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