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(-) Description

Title :  NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLATE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID.
 
Authors :  S. E. Greasley, M. M. Yamashita, H. Cai, S. J. Benkovic, D. L. Boger, I. A. Wilson
Date :  27 Jul 99  (Deposition) - 29 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Purine Biosynthesis, Anti-Cancer Agent, Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Greasley, M. M. Yamashita, H. Cai, S. J. Benkovic, D. L. Boger, I. A. Wilson
New Insights Into Inhibitor Design From The Crystal Structure And Nmr Studies Of Escherichia Coli Gar Transformylase In Complex With Beta-Gar And 10-Formyl-5, 8, 10-Trideazafolic Acid.
Biochemistry V. 38 16783 1999
PubMed-ID: 10606510  |  Reference-DOI: 10.1021/BI991888A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
    Chains: A, B
    EC Number: 2.1.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PURN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GAR2Ligand/IonGLYCINAMIDE RIBONUCLEOTIDE
2NHR2Ligand/Ion2-{4-[2-(2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL)-1-CARBOXY-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:64 , PHE A:88 , MET A:89 , ARG A:90 , ILE A:91 , LEU A:92 , VAL A:97 , ASN A:106 , HIS A:108 , LEU A:118 , VAL A:139 , THR A:140 , GLU A:142 , LEU A:143 , ASP A:144 , GAR A:221BINDING SITE FOR RESIDUE NHR A 220
2AC2SOFTWAREGLY A:11 , SER A:12 , ASN A:13 , GLY A:87 , PHE A:88 , MET A:89 , ILE A:107 , PRO A:109 , GLU A:173 , NHR A:220 , HOH A:225 , HOH A:232 , HOH A:269BINDING SITE FOR RESIDUE GAR A 221
3AC3SOFTWAREGLU A:131 , ARG B:64 , PHE B:88 , MET B:89 , ARG B:90 , ILE B:91 , LEU B:92 , VAL B:97 , ASN B:106 , HIS B:108 , LEU B:118 , VAL B:139 , THR B:140 , GLU B:142 , ASP B:144 , GAR B:223BINDING SITE FOR RESIDUE NHR B 222
4AC4SOFTWAREASN B:10 , GLY B:11 , SER B:12 , ASN B:13 , GLY B:87 , PHE B:88 , MET B:89 , ILE B:107 , PRO B:109 , GLU B:173 , NHR B:222 , HOH B:246 , HOH B:248 , HOH B:289 , HOH B:291BINDING SITE FOR RESIDUE GAR B 223

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C3E)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:112 -Pro A:113
2Leu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C3E)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.PUR3_ECOLI133-156
 		  2A:133-156
B:133-156

(-) Exons   (0, 0)

(no "Exon" information available for 1C3E)

(-) 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:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1c3ea_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1c3eA00 A:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c3e A   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1c3eb_ B: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1c3eB00 B:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: B:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c3e B   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 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 1C3E)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PUR3_ECOLI | P08179)
molecular function
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0004644    phosphoribosylglycinamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
    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.
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR3_ECOLI | P08179: 1c2t 1cdd 1cde 1gar 1grc 1jkx 2gar 3gar

(-) Related Entries Specified in the PDB File

1c2t 1C2T CONTAINS THE SAME PROTEIN COMPLEXED TO THE (10S)-10- FORMYL-TDAF AND BETA GAR