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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH HYPOXANTHINE
 
Authors :  M. Ho, K. Z. Hazleton, S. C. Almo, V. L. Schramm
Date :  24 Sep 10  (Deposition) - 28 Sep 11  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hypoxanthine, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Z. Hazleton, M. C. Ho, M. B. Cassera, K. Clinch, D. R. Crump, I. Rosario, E. F. Merino, S. C. Almo, P. C. Tyler, V. L. Schramm
Acyclic Immucillin Phosphonates: Second-Generation Inhibitors Of Plasmodium Falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase.
Chem. Biol. V. 19 721 2012
PubMed-ID: 22726686  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.04.012

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LACZ
    Organism Scientific: PLASMODIUM FALCIPARUM FCR-3/GAMBIA
    Organism Taxid: 5838
    Synonym: HGXPRTASE, HGXPRT, HGPRT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1HPA4Ligand/IonHYPOXANTHINE
2MG6Ligand/IonMAGNESIUM ION
3PO44Ligand/IonPHOSPHATE ION
4POP4Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:116 , ILE A:146 , ASP A:148 , LYS A:176 , PHE A:197 , VAL A:198 , ASP A:204 , HOH A:298 , HOH A:305BINDING SITE FOR RESIDUE HPA A 232
02AC2SOFTWARELYS A:77 , GLY A:78 , ARG A:112 , LYS A:114 , SER A:115 , TYR A:116 , ASP A:204 , ARG A:210 , MG A:235 , HOH A:237 , HOH A:238 , HOH A:259 , HOH A:285 , HOH A:298 , HOH A:304 , HOH A:305 , HOH A:418BINDING SITE FOR RESIDUE POP A 233
03AC3SOFTWARETYR A:116 , ASP A:148 , THR A:149 , GLY A:150 , LYS A:151 , THR A:152 , HOH A:253 , HOH A:269 , HOH A:304BINDING SITE FOR RESIDUE PO4 A 234
04AC4SOFTWAREASP A:204 , POP A:233 , HOH A:237 , HOH A:238 , HOH A:298BINDING SITE FOR RESIDUE MG A 235
05AC5SOFTWARETYR B:116 , ILE B:146 , ASP B:148 , LYS B:176 , PHE B:197 , VAL B:198 , ASP B:204 , PO4 B:234 , HOH B:299 , HOH B:307BINDING SITE FOR RESIDUE HPA B 232
06AC6SOFTWARELYS B:77 , GLY B:78 , ARG B:112 , LYS B:114 , SER B:115 , TYR B:116 , ASP B:204 , ARG B:210 , MG B:235 , HOH B:236 , HOH B:240 , HOH B:258 , HOH B:307 , HOH B:309BINDING SITE FOR RESIDUE POP B 233
07AC7SOFTWARETYR B:116 , ASP B:148 , THR B:149 , GLY B:150 , LYS B:151 , THR B:152 , HPA B:232 , HOH B:250 , HOH B:309 , HOH B:419BINDING SITE FOR RESIDUE PO4 B 234
08AC8SOFTWAREASP B:204 , POP B:233 , HOH B:236 , HOH B:240 , HOH B:299BINDING SITE FOR RESIDUE MG B 235
09AC9SOFTWARETYR C:116 , ILE C:146 , ASP C:148 , LYS C:176 , PHE C:197 , VAL C:198 , ASP C:204 , PO4 C:234 , HOH C:242 , HOH C:300BINDING SITE FOR RESIDUE HPA C 232
10BC1SOFTWARELYS C:77 , GLY C:78 , ARG C:112 , VAL C:113 , LYS C:114 , SER C:115 , TYR C:116 , ASP C:204 , ARG C:210 , MG C:235 , MG C:236 , HOH C:237 , HOH C:242 , HOH C:271 , HOH C:285 , HOH C:295 , HOH C:300 , HOH C:301 , HOH C:305BINDING SITE FOR RESIDUE POP C 233
11BC2SOFTWARETYR C:116 , ASP C:148 , THR C:149 , GLY C:150 , LYS C:151 , THR C:152 , HPA C:232 , HOH C:238 , HOH C:246 , HOH C:264 , HOH C:310BINDING SITE FOR RESIDUE PO4 C 234
12BC3SOFTWAREASP C:204 , POP C:233 , HOH C:240 , HOH C:241 , HOH C:242BINDING SITE FOR RESIDUE MG C 235
13BC4SOFTWAREPOP C:233 , HOH C:237 , HOH C:238 , HOH C:239 , HOH C:300 , HOH C:301BINDING SITE FOR RESIDUE MG C 236
14BC5SOFTWARETYR D:116 , ASP D:148 , THR D:149 , GLY D:150 , LYS D:151 , THR D:152 , HPA D:235 , HOH D:244 , HOH D:250 , HOH D:252BINDING SITE FOR RESIDUE PO4 D 232
15BC6SOFTWAREASP D:204 , POP D:236 , HOH D:237 , HOH D:238 , HOH D:239BINDING SITE FOR RESIDUE MG D 233
16BC7SOFTWAREPOP D:236 , HOH D:247 , HOH D:252 , HOH D:258 , HOH D:294 , HOH D:296BINDING SITE FOR RESIDUE MG D 234
17BC8SOFTWARETYR D:116 , ILE D:146 , ASP D:148 , LYS D:176 , PHE D:197 , VAL D:198 , ASP D:204 , PO4 D:232 , HOH D:238 , HOH D:258BINDING SITE FOR RESIDUE HPA D 235
18BC9SOFTWARELYS D:77 , GLY D:78 , ARG D:112 , LYS D:114 , SER D:115 , TYR D:116 , ASP D:204 , ARG D:210 , MG D:233 , MG D:234 , HOH D:237 , HOH D:238 , HOH D:239 , HOH D:247 , HOH D:253 , HOH D:258 , HOH D:288 , HOH D:289 , HOH D:296 , HOH D:311BINDING SITE FOR RESIDUE POP D 236

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OZF)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu A:76 -Lys A:77
2Leu B:76 -Lys B:77
3Leu C:76 -Lys C:77
4Leu D:76 -Lys D:77
5Ser D:129 -Glu D:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OZF)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.HGXR_PLAFG140-152
 
 
 		  4A:140-152
B:140-152
C:140-152
D:140-152

(-) Exons   (0, 0)

(no "Exon" information available for 3OZF)

(-) 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:233
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:233
                                 1                                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
           HGXR_PLAFG     - -----MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
               SCOP domains d3ozfa_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeee..hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozf A  -4 PRGSHMPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:234
                                  1                                                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
           HGXR_PLAFG     - ------MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
               SCOP domains d3ozfb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeeee.hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ozf B  -5 VPRGSHMPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    


Chain C from PDB  Type:PROTEIN  Length:228
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           HGXR_PLAFG     2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKAT 229
               SCOP domains d3ozfc_ C: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............ee..............hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeeee.hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR----------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ozf C   2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKAT 229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           HGXR_PLAFG     2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKAT 229
               SCOP domains d3ozfd_ D: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeee..hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR----------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ozf D   2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKAT 229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OZF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OZF)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (HGXR_PLAFG | P20035)
molecular function
    GO:0052657    guanine phosphoribosyltransferase activity    Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0004422    hypoxanthine phosphoribosyltransferase activity    Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0032263    GMP salvage    Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0032264    IMP salvage    Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
    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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HGXR_PLAFG | P20035: 1cjb 2vfa 3ozg

(-) Related Entries Specified in the PDB File

3ozg HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH S-SERME-IMMH PHOSPHONATE