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(-) Description

Title :  STRUCTURE OF URACIL PHOSPHORIBOSYL TRANSFERASE
 
Authors :  N. K. Lokanath, Riken Structural Genomics/Proteomics Initiative
Date :  06 Mar 07  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,D  (1x)
Biol. Unit 3:  B,C  (1x)
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, K. J. Pampa, T. Kamiya, N. Kunishima
Structure Of Uracil Phosphoribosyl Transferase
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
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CELL-FREE SYNTHESIS
    Synonym: UMP PYROPHOSPHORYLASE, UPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A  D
Biological Unit 3 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1SO419Ligand/IonSULFATE ION
Biological Unit 1 (1, 19)
No.NameCountTypeFull Name
1SO419Ligand/IonSULFATE ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 3 (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:1 , LYS A:2 , LEU A:169 , GLU A:170 , HIS A:173 , PRO A:174BINDING SITE FOR RESIDUE SO4 A 209
02AC2SOFTWARELYS B:1 , LYS B:2 , LEU B:169 , GLU B:170 , HIS B:173 , PRO B:174BINDING SITE FOR RESIDUE SO4 B 209
03AC3SOFTWARELYS C:1 , LYS C:2 , ILE C:166 , LEU C:169 , GLU C:170 , HIS C:173 , PRO C:174BINDING SITE FOR RESIDUE SO4 C 209
04AC4SOFTWARELYS D:1 , LYS D:2 , LEU D:169 , GLU D:170 , HIS D:173 , PRO D:174BINDING SITE FOR RESIDUE SO4 D 209
05AC5SOFTWAREARG A:103 , ALA A:134 , THR A:135 , GLY A:136 , GLY A:137 , SER A:138BINDING SITE FOR RESIDUE SO4 A 210
06AC6SOFTWAREARG B:103 , ALA B:134 , THR B:135 , GLY B:136 , GLY B:137 , SER B:138BINDING SITE FOR RESIDUE SO4 B 210
07AC7SOFTWAREALA C:134 , THR C:135 , GLY C:136 , GLY C:137 , SER C:138BINDING SITE FOR RESIDUE SO4 C 210
08AC8SOFTWAREARG D:103 , ALA D:134 , THR D:135 , GLY D:136 , GLY D:137 , SER D:138BINDING SITE FOR RESIDUE SO4 D 210
09AC9SOFTWARELYS A:69 , LYS A:70 , ARG A:95 , ARG A:124BINDING SITE FOR RESIDUE SO4 A 211
10BC1SOFTWARELYS C:69 , LYS C:70 , ARG C:95 , ARG C:124BINDING SITE FOR RESIDUE SO4 C 211
11BC2SOFTWARELYS D:69 , LYS D:70 , ARG D:95 , ARG D:124 , HOH D:226BINDING SITE FOR RESIDUE SO4 D 211
12BC3SOFTWAREARG A:78 , ALA A:79BINDING SITE FOR RESIDUE SO4 A 212
13BC4SOFTWAREARG B:78 , ALA B:79BINDING SITE FOR RESIDUE SO4 B 211
14BC5SOFTWARELEU C:77 , ARG C:78 , ALA C:79 , ARG C:103 , GLY C:201BINDING SITE FOR RESIDUE SO4 C 212
15BC6SOFTWARELEU D:77 , ARG D:78 , ALA D:79BINDING SITE FOR RESIDUE SO4 D 212
16BC7SOFTWARESER C:24 , THR C:25 , LYS D:70 , ARG D:95 , HOH D:220BINDING SITE FOR RESIDUE SO4 D 213
17BC8SOFTWAREARG C:95 , SER D:24 , THR D:25BINDING SITE FOR RESIDUE SO4 C 213
18BC9SOFTWAREARG A:95 , SER B:24 , THR B:25BINDING SITE FOR RESIDUE SO4 A 213
19CC1SOFTWARESER A:24 , THR A:25 , LYS B:70 , ARG B:95BINDING SITE FOR RESIDUE SO4 B 212

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:194 -Pro A:195
2Ile B:194 -Pro B:195
3Ile C:194 -Pro C:195
4Ile D:194 -Pro D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EHJ)

(-) 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:208
 aligned with UPP_ECOLI | P0A8F0 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_ECOLI     1 MKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 208
               SCOP domains d2ehja_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2ehjA00 A:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee.....eeee..hhhhhhhhhhhhhh...ee.eeeeee......eeeeeee...hhhh.eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhh...eeee.....ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehj A   1 KKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 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_ECOLI | P0A8F0 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_ECOLI     1 MKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 208
               SCOP domains d2ehjb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2ehjB00 B:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee.....eeee....hhhhhhhhhhhh...ee.eeeeeee....eeeeeeee...hhhhh.eeee..ee..hhhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehj B   1 KKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 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_ECOLI | P0A8F0 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_ECOLI     1 MKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 208
               SCOP domains d2ehjc_ C: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2ehjC00 C:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee.....eeee..hhhhhhhhhhhhhh...ee.eeee..........eeeee...hhhhh.eeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehj C   1 KKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 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_ECOLI | P0A8F0 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_ECOLI     1 MKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 208
               SCOP domains d2ehjd_ D: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2ehjD00 D:1-208  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee.....eeee....hhhhhhhhhhhh...ee.eee.............eee...hhhhh.eeee..ee..hhhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehj D   1 KKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKAHPDVELYTASIDQGLNEHGYIIPGLGDAGDKIFGTK 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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (UPP_ECOLI | P0A8F0)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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