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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI XGPRT IN COMPLEX WITH (3R,4S)-4-(GUANIN-9-YL)-3-HYDROXYPYRROLIDIN-1-N-YLACETYLPHOSPHONIC ACID
 
Authors :  D. T. Keough, D. Hockova, D. Rejman, P. Spacek, S. Vrbkova, M. Krecmerov W. S. Eng, H. Jans, N. P. West, L. M. J. Naesens, J. De Jersey, L. W. Gudda
Date :  12 Mar 13  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,H,I,J
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,H,I,J  (1x)
Keywords :  Xanthine-Guanine Phosphoribosyltransferase, Purine Salvage, Nucleoside Phosphonate, Antibacterial, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Keough, D. Hockova, D. Rejman, P. Spacek, S. Vrbkova, M. Krecmerova, W. S. Eng, H. Jans, N. P. West, L. M. Naesens, J. De Jersey, L. W. Guddat
Inhibition Of The Escherichia Coli 6-Oxopurine Phosphoribosyltransferases By Nucleoside Phosphonates: Potential For New Antibacterial Agents.
J. Med. Chem. V. 56 6967 2013
PubMed-ID: 23927482  |  Reference-DOI: 10.1021/JM400779N

(-) Compounds

Molecule 1 - XANTHINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D, E, H, I, J
    EC Number: 2.4.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GPT, ECMDS42_0227
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 1110693
    Strain: STR. K-12 SUBSTR. MDS42
    Synonym: XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEHIJ
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
13ZE8Ligand/Ion{2-[(3S,4R)-3-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-4-HYDROXYPYRROLIDIN-1-YL]-2-OXOETHYL}PHOSPHONICACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
13ZE4Ligand/Ion{2-[(3S,4R)-3-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-4-HYDROXYPYRROLIDIN-1-YL]-2-OXOETHYL}PHOSPHONICACID
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
13ZE4Ligand/Ion{2-[(3S,4R)-3-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-4-HYDROXYPYRROLIDIN-1-YL]-2-OXOETHYL}PHOSPHONICACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:90 , VAL A:91 , ASP A:92 , THR A:93 , GLY A:94 , GLY A:95 , THR A:96 , LYS A:115 , THR A:133 , TRP A:134 , ILE A:135 , HOH A:328 , HOH A:360BINDING SITE FOR RESIDUE 3ZE A 201
2AC2SOFTWARELEU B:90 , VAL B:91 , ASP B:92 , THR B:93 , GLY B:94 , GLY B:95 , THR B:96 , LYS B:115 , THR B:133 , TRP B:134 , ILE B:135 , HOH B:349BINDING SITE FOR RESIDUE 3ZE B 201
3AC3SOFTWARELEU C:90 , VAL C:91 , ASP C:92 , THR C:93 , GLY C:94 , GLY C:95 , THR C:96 , LYS C:115 , THR C:133 , TRP C:134 , ILE C:135 , HOH C:337BINDING SITE FOR RESIDUE 3ZE C 201
4AC4SOFTWAREVAL D:91 , ASP D:92 , THR D:93 , GLY D:94 , GLY D:95 , THR D:96 , LYS D:115 , THR D:133 , TRP D:134 , ILE D:135 , HOH D:334 , HOH D:353BINDING SITE FOR RESIDUE 3ZE D 201
5AC5SOFTWARELEU E:90 , VAL E:91 , ASP E:92 , THR E:93 , GLY E:94 , GLY E:95 , THR E:96 , LYS E:115 , THR E:133 , TRP E:134 , ILE E:135BINDING SITE FOR RESIDUE 3ZE E 201
6AC6SOFTWARELEU H:90 , VAL H:91 , ASP H:92 , THR H:93 , GLY H:94 , GLY H:95 , THR H:96 , LYS H:115 , THR H:133 , TRP H:134 , ILE H:135 , HOH H:329 , HOH H:361 , HOH H:364 , HOH H:369BINDING SITE FOR RESIDUE 3ZE H 201
7AC7SOFTWAREGLY A:79 , LEU I:90 , VAL I:91 , ASP I:92 , THR I:93 , GLY I:94 , GLY I:95 , THR I:96 , LYS I:115 , THR I:133 , TRP I:134 , ILE I:135 , HOH I:309 , HOH I:349 , HOH I:372BINDING SITE FOR RESIDUE 3ZE I 201
8AC8SOFTWARELEU J:90 , VAL J:91 , ASP J:92 , THR J:93 , GLY J:94 , GLY J:95 , THR J:96 , LYS J:115 , THR J:133 , TRP J:134 , ILE J:135 , HOH J:343BINDING SITE FOR RESIDUE 3ZE J 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Met A:24 -Pro A:25
2Ser A:36 -Arg A:37
3Met B:24 -Pro B:25
4Ser B:36 -Arg B:37
5Met C:24 -Pro C:25
6Ser C:36 -Arg C:37
7Met D:24 -Pro D:25
8Ser D:36 -Arg D:37
9Met E:24 -Pro E:25
10Ser E:36 -Arg E:37
11Met H:24 -Pro H:25
12Ser H:36 -Arg H:37
13Met I:24 -Pro I:25
14Ser I:36 -Arg I:37
15Met J:24 -Pro J:25
16Ser J:36 -Arg J:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JLS)

(-) Sequences/Alignments

Asymmetric 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh...eeee........eeeeeeee..hhhhhhhhhhh...eeeeeee.hhhhhhh.eeeee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls A   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        79        89        99       109       119       129       139       149   
                                                                                     61|                                                                         
                                                                                      79                                                                         


Chain B from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh....eeee..........eeeeeeee..hhhhhhhhhhh...eeeeeee...hhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls B   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        62|       87        97       107       117       127       137       147     
                                                                                      62|                                                                          
                                                                                       78                                                                          


Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh...eeee........eeeeeeee..hhhhhhhhhhh...eeeeeee...hhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls C   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        79        89        99       109       119       129       139       149   
                                                                                     61|                                                                         
                                                                                      79                                                                         


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhh.hhhhh.eeeee...hhhhhhhhhhhhh...eeee........eeeeeeee..hhhhhhhhhhh...eeeeeee...hhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls D   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        62|       89        99       109       119       129       139       149   
                                                                                      62|                                                                        
                                                                                       80                                                                        


Chain E from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhh.hhhhh.eeeee...hhhhhhhhhhhhh...eeee.........eeeeeeee..hhhhhhhhhhh...eeeeeee...hhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls E   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        62|       88        98       108       118       128       138       148    
                                                                                      62|                                                                         
                                                                                       79                                                                         


Chain H from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh...eeee........eeeeeeee..hhhhhhhhhhh...eeeeeee.hhhhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls H   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        62|       89        99       109       119       129       139       149   
                                                                                      62|                                                                        
                                                                                       80                                                                        


Chain I from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh...eeee......eeeeeeee..hhhhhhhhhhh...eeeeeee...hhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls I   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCIDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52       |81        91       101       111       121       131       141       151 
                                                                                    60|                                                                        
                                                                                     80                                                                        


Chain J from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhh...eeeee........eeeeeeee..hhhhhhhhhhh...eeeeeee.hhhhhhh....ee.....eeehhh.eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jls J   3 EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR 152
                                    12        22        32        42        52        62||      88        98       108       118       128       138       148    
                                                                                       63|                                                                        
                                                                                        80
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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  (0, 0)

(no "SCOP Domain" information available for 4JLS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JLS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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4jit