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(-) Description

Title :  CRYSTAL STRUCTURE OF PROJECT JW0458 FROM ESCHERICHIA COLI
 
Authors :  K. Shimizu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Sep 06  (Deposition) - 04 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 :  K. Shimizu, N. Kunishima
Crystal Structure Of Jw0458 From Escherichia Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.7
    Engineered: YES
    Expression System Plasmid: PX060316-06
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Other Details: CELL FREE
    Strain: K12, W3110
    Synonym: APRT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1032 , HOH A:1044 , HOH A:1096 , HOH A:1171 , HOH A:1219 , HOH A:1252BINDING SITE FOR RESIDUE MG A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DY0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:21 -Pro A:22
2Glu A:64 -Ala A:65
3Tyr B:21 -Pro B:22
4Glu B:64 -Ala B:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DY0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT_ECOLI122-134
 		  2A:122-134
B:122-134

(-) Exons   (0, 0)

(no "Exon" information available for 2DY0)

(-) 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:182
 aligned with APT_ECOLI | P69503 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
            APT_ECOLI     2 TATAQQLEYLKNSIKSIQDYPKPGILFRDVTSLLEDPKAYALSIDLLVERYKNAGITKVVGTEARGFLFGAPVALGLGVGFVPVRKPGKLPRETISETYDLEYGTDQLEIHVDAIKPGDKVLVVDDLLATGGTIEATVKLIRRLGGEVADAAFIINLFDLGGEQRLEKQGITSYSLVPFPGH 183
               SCOP domains d2dy0a_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains 2dy0A00 A:2-183  [code=3.40.50.2020, no name defined]                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.eeeee.........eeeeeeee..eeeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhh...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dy0 A   2 TATAQQLEYLKNSIKSIQDYPKPGILFRDVTSLLEDPKAYALSIDLLVERYKNAGITKVVGTEARGFLFGAPVALGLGVGFVPVRKPGKLPRETISETYDLEYGTDQLEIHVDAIKPGDKVLVVDDLLATGGTIEATVKLIRRLGGEVADAAFIINLFDLGGEQRLEKQGITSYSLVPFPGH 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with APT_ECOLI | P69503 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
            APT_ECOLI     3 ATAQQLEYLKNSIKSIQDYPKPGILFRDVTSLLEDPKAYALSIDLLVERYKNAGITKVVGTEARGFLFGAPVALGLGVGFVPVRKPGKLPRETISETYDLEYGTDQLEIHVDAIKPGDKVLVVDDLLATGGTIEATVKLIRRLGGEVADAAFIINLFDLGGEQRLEKQGITSYSLVPFPGH 183
               SCOP domains d2dy0b_ B: automated matches                                                                                                                                                          SCOP domains
               CATH domains 2dy0B00 B:3-183  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeee.......eeeehhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh.eeeee.........eeeeeeee..eeeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhh...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dy0 B   3 ATAQQLEYLKNSIKSIQDYPKPGILFRDVTSLLEDPKAYALSIDLLVERYKNAGITKVVGTEARGFLFGAPVALGLGVGFVPVRKPGKLPRETISETYDLEYGTDQLEIHVDAIKPGDKVLVVDDLLATGGTIEATVKLIRRLGGEVADAAFIINLFDLGGEQRLEKQGITSYSLVPFPGH 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DY0)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (APT_ECOLI | P69503)
molecular function
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    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: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).
biological process
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    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:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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