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(-) Description

Title :  BACILLUS SUBTILIS XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GUANOSINE 5'-MONOPHOSPHATE (GMP)
 
Authors :  S. Arent, A. Kadziola, S. Larsen, J. Neuhard, K. F. Jensen
Date :  06 Feb 06  (Deposition) - 20 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Type 1 Phosphoribosyltransferase, Gmp Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Arent, A. Kadziola, S. Larsen, J. Neuhard, K. F. Jensen
The Extraordinary Specificity Of Xanthine Phosphoribosyltransferase From Bacillus Subtilis Elucidated By Reaction Kinetics, Ligand Binding, And Crystallography
Biochemistry V. 45 6615 2006
PubMed-ID: 16716072  |  Reference-DOI: 10.1021/BI060287Y

(-) Compounds

Molecule 1 - XANTHINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUHE23-2
    Expression System Strain: NF1830
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: XPT
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:19 , LEU A:20 , ASN A:27 , PHE A:99 , THR A:100 , ASP A:125 , PHE A:126 , ALA A:128 , ASN A:129 , GLY A:130 , GLN A:131 , ALA A:132 , LYS A:156 , HOH A:809 , HOH A:814 , HOH A:825 , HOH A:860BINDING SITE FOR RESIDUE 5GP A 200
2AC2SOFTWAREVAL B:19 , LEU B:20 , ASN B:27 , PHE B:99 , THR B:100 , ASP B:124 , ASP B:125 , PHE B:126 , ALA B:128 , ASN B:129 , GLY B:130 , GLN B:131 , ALA B:132 , LYS B:156 , HOH B:801 , HOH B:802 , HOH B:803 , HOH B:805 , HOH B:919BINDING SITE FOR RESIDUE 5GP B 201
3AC3SOFTWAREASP B:116 , GLN B:117 , ASP B:118 , SER B:146 , GLU B:182BINDING SITE FOR RESIDUE GOL B 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:58 -Ser A:59
2Glu B:58 -Ser B:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FXV)

(-) 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:190
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
            XPT_BACSU     1 MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQ 190
               SCOP domains d2fxva_ A: Xanthine phosphoribosyltransferase                                                                                                                                                  SCOP domains
               CATH domains 2fxvA00 A:1-190  [code=3.40.50.2020, no name defined]                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhee.....ee.......eehhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeeeeee........eeeeeee......eeeeeee.hhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhh..eeeeeeeeehhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fxv A   1 MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQ 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with XPT_BACSU | P42085 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
            XPT_BACSU     1 MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQ 190
               SCOP domains d2fxvb_ B: Xanthine phosphoribosyltransferase                                                                                                                                                  SCOP domains
               CATH domains 2fxvB00 B:1-190  [code=3.40.50.2020, no name defined]                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhee.....ee.......eehhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeeeeee.........eeeeee......eeeeeehhhhh....eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhh...eeeeeeeeehhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fxv B   1 MEALKRKIEEEGVVLSDQVLKVDSFLNHQIDPLLMQRIGDEFASRFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARKHKSLTLTDNLLTASVYSFTKQTESQIAVSGTHLSDQDHVLIIDDFLANGQAAHGLVSIVKQAGASIAGIGIVIEKSFQPGRDELVKLGYRVESLARIQSLEEGKVSFVQ 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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 2FXV)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (XPT_BACSU | P42085)
molecular function
    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).
    GO:0000310    xanthine phosphoribosyltransferase activity    Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + xanthine = (9-D-ribosylxanthine)-5'-phosphate + diphosphate.
biological process
    GO:0032265    XMP salvage    Any process which produces xanthosine monophosphate 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.
    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.
    GO:0046110    xanthine metabolic process    The chemical reactions and pathways involving xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids.
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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        XPT_BACSU | P42085: 1y0b

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