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(-) Description

Title :  HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH [(2-((GUANINE-9H-YL)METHYL)PROPANE-1,3-DIYL)BIS(OXY)]BIS(METHYLENE)) DIPHOSPHONIC ACID
 
Authors :  L. W. Guddat, D. T. Keough, D. Hockova
Date :  22 Dec 12  (Deposition) - 27 Mar 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gmp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Keough, P. Spacek, D. Hockova, T. Tichy, S. Vrbkova, L. Slavetinska, Z. Janeba, L. Naesens, M. D. Edstein, M. Chavchich, T. H. Wang, J. Jersey, L. W. Guddat
Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group Are Potent Inhibitors Of 6-Oxopurine Phosphoribosyltransferases And Have Antimalarial Activity
J. Med. Chem. V. 56 2513 2013
PubMed-ID: 23448281  |  Reference-DOI: 10.1021/JM301893B

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HUMAN HGPRT, UNP RESIDUES 4-217
    Gene: HPRT1, HPRT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGPRT, HGPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
3SV24Ligand/Ion[{2-[(GUANINE-9-YL)METHYL]PROPANE-1,3-DIYL}BIS(OXYMETHYLENE)]BIS(PHOSPHONIC ACID)

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:102 , ASP A:137 , THR A:138 , GLY A:139 , LYS A:140 , THR A:141 , LYS A:165 , LYS A:185 , PHE A:186 , VAL A:187 , ASP A:193 , SO4 A:302 , MG A:304 , HOH A:405 , HOH A:406 , HOH A:407 , HOH A:408 , HOH A:410 , HOH A:421 , HOH A:431 , HOH A:445 , HOH A:449BINDING SITE FOR RESIDUE SV2 A 301
02AC2SOFTWARELYS A:68 , GLY A:69 , ASP A:193 , ARG A:199 , SV2 A:301 , MG A:304 , HOH A:402 , HOH A:404 , HOH A:409 , HOH A:411 , HOH A:467BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREGLU A:133 , ASP A:134 , HOH A:401 , HOH A:402 , HOH A:403 , HOH A:404BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWAREASP A:193 , SV2 A:301 , SO4 A:302 , HOH A:405 , HOH A:406 , HOH A:407BINDING SITE FOR RESIDUE MG A 304
05AC5SOFTWAREASP B:137 , THR B:138 , GLY B:139 , LYS B:140 , THR B:141 , LYS B:165 , LYS B:185 , PHE B:186 , VAL B:187 , ASP B:193 , SO4 B:303 , MG B:304 , HOH B:409 , HOH B:416 , HOH B:429 , HOH B:450 , HOH B:458BINDING SITE FOR RESIDUE SV2 B 301
06AC6SOFTWAREGLU B:133 , ASP B:134 , HOH B:403 , HOH B:404 , HOH B:405 , HOH B:470BINDING SITE FOR RESIDUE MG B 302
07AC7SOFTWARELYS B:68 , GLY B:69 , ASP B:193 , ARG B:199 , SV2 B:301 , MG B:304 , HOH B:403 , HOH B:421 , HOH B:437 , HOH B:470BINDING SITE FOR RESIDUE SO4 B 303
08AC8SOFTWAREASP B:193 , SV2 B:301 , SO4 B:303 , HOH B:415 , HOH B:423 , HOH B:450BINDING SITE FOR RESIDUE MG B 304
09AC9SOFTWAREILE C:135 , ASP C:137 , THR C:138 , GLY C:139 , LYS C:140 , THR C:141 , LYS C:165 , LYS C:185 , PHE C:186 , VAL C:187 , ASP C:193 , MG C:303 , SO4 C:304 , HOH C:409 , HOH C:425 , HOH C:434BINDING SITE FOR RESIDUE SV2 C 301
10BC1SOFTWAREGLU C:133 , ASP C:134 , HOH C:401 , HOH C:402 , HOH C:403 , HOH C:467BINDING SITE FOR RESIDUE MG C 302
11BC2SOFTWAREASP C:193 , GLU C:196 , ARG C:199 , SV2 C:301 , SO4 C:304BINDING SITE FOR RESIDUE MG C 303
12BC3SOFTWARELYS C:68 , GLY C:69 , ASP C:193 , ARG C:199 , SV2 C:301 , MG C:303 , HOH C:401 , HOH C:411BINDING SITE FOR RESIDUE SO4 C 304
13BC4SOFTWAREASP D:193 , SV2 D:302 , SO4 D:304 , HOH D:433 , HOH D:460 , HOH D:465BINDING SITE FOR RESIDUE MG D 301
14BC5SOFTWAREASP D:137 , THR D:138 , GLY D:139 , LYS D:140 , THR D:141 , LYS D:165 , LYS D:185 , PHE D:186 , VAL D:187 , ASP D:193 , MG D:301 , SO4 D:304 , HOH D:411 , HOH D:427 , HOH D:447 , HOH D:465BINDING SITE FOR RESIDUE SV2 D 302
15BC6SOFTWAREGLU D:133 , ASP D:134 , HOH D:401 , HOH D:402 , HOH D:403 , HOH D:404BINDING SITE FOR RESIDUE MG D 303
16BC7SOFTWARELYS D:68 , GLY D:69 , ASP D:193 , ARG D:199 , MG D:301 , SV2 D:302 , HOH D:402 , HOH D:403 , HOH D:455BINDING SITE FOR RESIDUE SO4 D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IJQ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Leu B:67 -Lys B:68
3Leu C:67 -Lys C:68
4Leu D:67 -Lys D:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IJQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IJQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4IJQ)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains d4ijqa_ A: Hypoxanthine-guanine PRTase (HGPRTase)                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ijq A   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       119       129       139       149       159       169       179       189       199       209        
                                                                                                                            102|                                                                                                  
                                                                                                                             119                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains d4ijqb_ B: Hypoxanthine-guanine PRTase (HGPRTase)                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijq B   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       114       124       134       144       154       164       174       184       194       204       214   
                                                                                                                            102|                                                                                                       
                                                                                                                             114                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4ijqc_ C: Hypoxanthine-guanine PRTase (HGPRTase)                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeeeeeeee...eee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee.....................eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijq C   5 PGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    14        24        34        44        54        64        74        84        94       104|      122       132       142       152       162       172       182       192       202       212     
                                                                                                                             104|                                                                                                        
                                                                                                                              113                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains d4ijqd_ D: Hypoxanthine-guanine PRTase (HGPRTase)                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeeeeeee...ee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ijq D   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       113       123       133       143       153       163       173       183       193       203       213    
                                                                                                                            102|                                                                                                        
                                                                                                                             113
   Legend:   → Mismatch (orange background)
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  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 4IJQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IJQ)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ijq
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  HPRT_HUMAN | P00492
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 Related Entries

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

UniProtKB/Swiss-Prot
        HPRT_HUMAN | P00492: 1bzy 1d6n 1hmp 1z7g 2vfa 3gep 3ggc 3ggj 4kn6 4rab 4rac 4rad 4ran 4rao 4raq 5brn 5bsk 5hia

(-) Related Entries Specified in the PDB File

1bzy HUMAN HGPRT IN COMPLEX WITH AN INHIBITOR
1cjb MALARIAL HGPRT IN COMPLEX WITH AN INHIBITOR
1hmp HUMAN HGPRT IN COMPLEX WITH GMP
3gep HUMAN HGPRT IN COMPLEX WITH AN INHIBITOR