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(-) Description

Title :  CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH PHOSPHATE AND TRIS MOLECULE
 
Authors :  T. C. Appleby, I. I. Mathews, M. Porcelli, G. Cacciapuoti, S. E. Ealick
Date :  15 Jun 01  (Deposition) - 26 Oct 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Alpha-Beta Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Appleby, I. I. Mathews, M. Porcelli, G. Cacciapuoti, S. E. Ealick
Three-Dimensional Structure Of A Hyperthermophilic 5'-Deoxy-5'-Methylthioadenosine Phosphorylase From Sulfolobus Solfataricus.
J. Biol. Chem. V. 276 39232 2001
PubMed-ID: 11489901  |  Reference-DOI: 10.1074/JBC.M105694200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-METHYLTHIOADENOSINE PHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: MTA PHOSPHORYLASE;
MTAP

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION
2TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:21 , ARG A:25 , ARG A:43 , ARG A:86 , GLY A:88 , THR A:89 , TRS A:270 , HOH A:283BINDING SITE FOR RESIDUE PO4 A 250
2AC2SOFTWAREGLY B:21 , ARG B:25 , ARG B:86 , GLY B:88 , THR B:89 , TRS B:275 , HOH B:288 , ARG C:43BINDING SITE FOR RESIDUE PO4 B 255
3AC3SOFTWAREARG B:43 , GLY C:21 , ARG C:25 , ARG C:86 , GLY C:88 , THR C:89 , TRS C:280 , HOH C:289BINDING SITE FOR RESIDUE PO4 C 260
4AC4SOFTWAREHIS A:5 , ARG A:86 , THR A:89 , GLU A:180 , MET A:181 , GLU A:182 , PO4 A:250BINDING SITE FOR RESIDUE TRS A 270
5AC5SOFTWAREARG B:86 , THR B:89 , GLU B:180 , MET B:181 , GLU B:182 , PO4 B:255 , HIS C:5BINDING SITE FOR RESIDUE TRS B 275
6AC6SOFTWAREHIS B:5 , ARG C:86 , THR C:89 , GLU C:180 , MET C:181 , GLU C:182 , PO4 C:260BINDING SITE FOR RESIDUE TRS C 280

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:125 -C:125
2B:125 -B:125

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JE0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JE0)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.PNPH_SULSO61-76
 
 		  3A:61-76
B:61-76
C:61-76
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.PNPH_SULSO61-76
 
 		  6A:61-76
B:61-76
C:61-76

(-) Exons   (0, 0)

(no "Exon" information available for 1JE0)

(-) 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:226
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PNPH_SULSO     3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1je0a_ A: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                   SCOP domains
               CATH domains 1je0A00 A:3-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee..--------hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1je0 A   3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLA--------EELEKSVMDGAKAVLDTLTS 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     |   -    |  222       232    
                                                                                                                                                                                                                                       208      217                   


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PNPH_SULSO     3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1je0b_ B: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                   SCOP domains
               CATH domains 1je0B00 B:3-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee..--------hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1je0 B   3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLA--------EELEKSVMDGAKAVLDTLTS 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     |   -    |  222       232    
                                                                                                                                                                                                                                       208      217                   


Chain C from PDB  Type:PROTEIN  Length:227
 aligned with PNPH_SULSO | P50389 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
           PNPH_SULSO     3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLAKGGIWITKEELEKSVMDGAKAVLDTLTS 236
               SCOP domains d1je0c_ C: 5'-deoxy-5'-methylthioadenosine phosphorylase                                                                                                                                                                                   SCOP domains
               CATH domains 1je0C00 C:3-236  [code=3.40.50.1580, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeee...hhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhh..eeeee.hhhhhhhhhhhhh.eeeeeeeeeee..-------hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1je0 C   3 PVHILAKKGEVAERVLVVGDPGRARLLSTLLQNPKLTNENRGFLVYTGKYNGETVSIATHGIGGPSIAIVLEELAMLGANVFIRYGTTGALVPYINLGEYIIVTGASYNQGGLFYQYLRDNACVASTPDFELTNKLVTSFSKRNLKYYVGNVFSSDAFYAEDEEFVKKWSSRGNIAVEMECATLFTLSKVKGWKSATVLVVSDNLA-------KEELEKSVMDGAKAVLDTLTS 236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     |   -   |   222       232    
                                                                                                                                                                                                                                       208     216
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JE0)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PNPH_SULSO | P50389)
molecular function
    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:0004731    purine-nucleoside phosphorylase activity    Catalysis of the reaction: purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
    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:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    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).

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  PNPH_SULSO | P50389
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  2.4.2.28
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 Related Entries

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

UniProtKB/Swiss-Prot
        PNPH_SULSO | P50389: 1jds 1jdt 1jdu 1jdv 1jdz 1je1 1jp7 1jpv

(-) Related Entries Specified in the PDB File

1jds NATIVE COMPLEX
1jdt COMPLEXED WITH PHOSPHATE
1jdu COMPLEXED WITH GUANOSINE AND SULFATE
1jdv COMPLEXED WITH PHOSPHATE (SPACE GROUP: C2221)
1jdz COMPLEXED WITH FORMYCIN B AND SULFATE
1je0 COMPLEXED WITH ADENOSINE AND SULFATE
1je1 COMPLEXED WITH MTA AND SULFATE