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(-) Description

Title :  PURINE NUCLEOSIDE PHOSPHORYLASE FROM CELLULOMONAS SP. IN COMPLEX WITH PHOSPHATE
 
Authors :  J. Tebbe, A. Bzowska, B. Wielgus-Kutrowska, W. Schroeder, Z. Kazimierczuk, D. Shugar, W. Saenger, G. Koellner
Date :  13 Jul 99  (Deposition) - 12 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Enzyme, Purine Nucleoside Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Tebbe, A. Bzowska, B. Wielgus-Kutrowska, W. Schroder, Z. Kazimierczuk, D. Shugar, W. Saenger, G. Koellner
Crystal Structure Of The Purine Nucleoside Phosphorylase (Pnp) From Cellulomonas Sp. And Its Implication For The Mechanism Of Trimeric Pnps.
J. Mol. Biol. V. 294 1239 1999
PubMed-ID: 10600382  |  Reference-DOI: 10.1006/JMBI.1999.3327
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENTOSYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.4.2.1
    Fragment: RESIDUES 9-282
    Organism Scientific: CELLULOMONAS SP.
    Organism Taxid: 40001

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:46 , ARG C:103 , HIS C:105 , ASN C:134 , GLY C:135 , SER C:223 , HOH C:427BINDING SITE FOR RESIDUE PO4 C 301
2AC2SOFTWAREGLY B:45 , SER B:46 , ARG B:103 , HIS B:105 , ASN B:134 , GLY B:135 , SER B:223 , HOH B:367 , HOH B:531BINDING SITE FOR RESIDUE PO4 B 302
3AC3SOFTWAREGLY A:45 , SER A:46 , ARG A:103 , HIS A:105 , ASN A:134 , GLY A:135 , SER A:223 , HOH A:537BINDING SITE FOR RESIDUE PO4 A 303
4AC4SOFTWAREGLU A:53 , GLY B:126 , GLU B:128 , HOH B:452 , HOH B:453 , HOH B:478 , HOH B:542BINDING SITE FOR RESIDUE CA B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QE5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:200 -Pro A:201
2Gly B:200 -Pro B:201
3Gly C:200 -Pro C:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QE5)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_MTAP_2PS01240 Purine and other phosphorylases family 2 signature.PUNA_CELSP98-139
 
 		  3A:98-139
B:98-139
C:98-139

(-) Exons   (0, 0)

(no "Exon" information available for 1QE5)

(-) 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:266
 aligned with PUNA_CELSP | P81989 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
           PUNA_CELSP     9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFSAPAVAGHLSVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
               SCOP domains d1qe5a_ A: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qe5A00 A:9-282  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....eeee.............eeeeeee.hhh....--------.eeeeeeee.....eeeeee.....hhhhh.hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee...................hhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhh..eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PNP_MTAP_2  PDB: A:98-139 UniProt: 98-139 ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qe5 A   9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFS--------SVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
                                    18        28        38        48        58        68  |      - |      88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
                                                                                         71       80                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with PUNA_CELSP | P81989 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
           PUNA_CELSP     9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFSAPAVAGHLSVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
               SCOP domains d1qe5b_ B: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qe5B00 B:9-282  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....eeee.............eeeeeee.hhh....--------.eeeeeeee.....eeeeee.....hhhhh.hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee...................hhhhhhhhhhhh....eeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PNP_MTAP_2  PDB: B:98-139 UniProt: 98-139 ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qe5 B   9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFS--------SVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
                                    18        28        38        48        58        68  |      - |      88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
                                                                                         71       80                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:266
 aligned with PUNA_CELSP | P81989 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
           PUNA_CELSP     9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFSAPAVAGHLSVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
               SCOP domains d1qe5c_ C: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qe5C00 C:9-282  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) ------------------------------PNP_UDP_1-1qe5C01 C:39-281                                                                                                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) ------------------------------PNP_UDP_1-1qe5C02 C:39-281                                                                                                                                                                                                                         - Pfam domains (2)
           Pfam domains (3) ------------------------------PNP_UDP_1-1qe5C03 C:39-281                                                                                                                                                                                                                         - Pfam domains (3)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....eeee.............eeeeeee.hhh....--------.eeeeeeee.....eeeeeee....hhhhh.hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeee...................hhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhh..eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PNP_MTAP_2  PDB: C:98-139 UniProt: 98-139 ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qe5 C   9 PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFS--------SVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR 282
                                    18        28        38        48        58        68  |      - |      88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
                                                                                         71       80
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PUNA_CELSP | P81989)
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:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PUNA_CELSP | P81989: 1c3x

(-) Related Entries Specified in the PDB File

1a69 PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN B AND SULPHATE
1vfn PURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH HYPOXANTHINE