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(-) Description

Title :  CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE (TM1596) FROM THERMOTOGA MARITIMA AT 2.01 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Sep 04  (Deposition) - 12 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Tm1596, Purine Nucleoside Phosphorylase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Purine Nucleoside Phosphorylase (Tm1596) From Thermotoga Maritima At 2. 01 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PURINE NUCLEOSIDE PHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1596
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 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
1GUN3Ligand/IonGUANINE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:322 , HOH B:358 , HOH B:391 , HOH B:397BINDING SITE FOR RESIDUE MG B 266
2AC2SOFTWAREALA A:111 , ALA A:112 , GLY A:113 , VAL A:180 , TYR A:185 , GLU A:186 , VAL A:202 , GLY A:203 , MET A:204 , THR A:227 , ASN A:228 , HOH A:339BINDING SITE FOR RESIDUE GUN A 300
3AC3SOFTWAREALA B:111 , ALA B:112 , GLY B:113 , VAL B:180 , GLU B:186 , VAL B:202 , GLY B:203 , MET B:204 , THR B:227 , ASN B:228 , HOH B:332BINDING SITE FOR RESIDUE GUN B 300
4AC4SOFTWAREALA C:111 , ALA C:112 , GLY C:113 , VAL C:180 , TYR C:185 , GLU C:186 , VAL C:202 , GLY C:203 , MET C:204 , THR C:227 , ASN C:228 , HOH C:322 , HOH C:345BINDING SITE FOR RESIDUE GUN C 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:182 -Pro A:183
2Gly B:182 -Pro B:183
3Gly C:182 -Pro C:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VMK)

(-) Exons   (0, 0)

(no "Exon" information available for 1VMK)

(-) 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:249
 aligned with Q9X1T2_THEMA | Q9X1T2 from UniProtKB/TrEMBL  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q9X1T2_THEMA     1 MMKKIEEARTFISERTNLSPDILIILGSGFGPFIEKVEDPVIIDYKDIPHFPQPTVEGHSGKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGITHGRLSHEEVVRTTKMAQGKIEKALTTAVEVF 265
               SCOP domains d1vmka_ A: Purine nucleosid   e phosphorylase, PNP                                                                                                                                                                                                                        SCOP domains
               CATH domains 1vmkA00 A:1-265  [code=3.40   .50.1580, no name defi        ned]                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......eeeee.---.......eeeeeee.hhh....--------.eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..........................hhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhhh.eeeeeeeeeee....-----hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vmk A   1 MMKKIEEARTFISERTNLSPDILIILG---GPFIEKVEDPVIIDYKDIPHFP--------GKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGI-----SHEEVVRTTKMAQGKIEKALTTAVEVF 265
                                    10        20      |  -|       40        50 |       -|       70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  |    240       250       260     
                                                     27  31                   52       61                                                                                                                                                                         233   239                          


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with Q9X1T2_THEMA | Q9X1T2 from UniProtKB/TrEMBL  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q9X1T2_THEMA     1 MMKKIEEARTFISERTNLSPDILIILGSGFGPFIEKVEDPVIIDYKDIPHFPQPTVEGHSGKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGITHGRLSHEEVVRTTKMAQGKIEKALTTAVEVF 265
               SCOP domains d1vmkb_ B: Purine nucleoside   phosphorylase, PNP                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vmkB00 B:1-265  [code=3.40.  50.1580, no name defin        ed]                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......eeeee..--hhhhhhheeeeeee.hhh....--------.eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee.........................hhhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee....-----hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vmk B   1 MMKKIEEARTFISERTNLSPDILIILGS--GPFIEKVEDPVIIDYKDIPHFP--------GKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGI-----SHEEVVRTTKMAQGKIEKALTTAVEVF 265
                                    10        20       | -|       40        50 |       -|       70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  |    240       250       260     
                                                      28 31                   52       61                                                                                                                                                                         233   239                          


Chain C from PDB  Type:PROTEIN  Length:241
 aligned with Q9X1T2_THEMA | Q9X1T2 from UniProtKB/TrEMBL  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q9X1T2_THEMA     1 MMKKIEEARTFISERTNLSPDILIILGSGFGPFIEKVEDPVIIDYKDIPHFPQPTVEGHSGKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGITHGRLSHEEVVRTTKMAQGKIEKALTTAVEVF 265
               SCOP domains d1vmkc_ C: Purine nucleosid     e phosphorylase, PNP                                                                                                                                                                                                                      SCOP domains
               CATH domains 1vmkC00 C:1-265  [code=3.40     .50.1580, no name de        fined]                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --------------------PNP_UDP     _1-1vmkC01 C:21-263                                                                                                                                                                                                                    -- Pfam domains (1)
           Pfam domains (2) --------------------PNP_UDP     _1-1vmkC02 C:21-263                                                                                                                                                                                                                    -- Pfam domains (2)
           Pfam domains (3) --------------------PNP_UDP     _1-1vmkC03 C:21-263                                                                                                                                                                                                                    -- Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhh.......eeeee.-----.....eeeeeee.hhh....--------.eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee.........................hhhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.....-----------....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vmk C   1 MMKKIEEARTFISERTNLSPDILIILG-----FIEKVEDPVIIDYKDIPHFP--------GKLVFGRISDKPVMIMAGRFHLYEGHDPATVAFPVYLAKYVGVKGVVVTNAAGAINPEFKPGEIILVRDIINFMFRNPLRGPNDEKIGPRFPDMSSVVDPEWARKIQERLSLKEGVYIGVLGPSYETPAEIRVFEKLGADLVGMSTVPEVIAAKHCGLKVVVFSCVTNMAAGIT-----------TTKMAQGKIEKALTTAVEVF 265
                                    10        20      |  -  |     40        50 |       -|       70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   |     -     | 250       260     
                                                     27    33                 52       61                                                                                                                                                                          234         246
   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  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q9X1T2_THEMA | Q9X1T2)
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).
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).
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them 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.

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