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(-) Description

Title :  THE STRUCTURE OF HUMAN GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE IN COMPLEX WITH 10R-METHYLTHIO-DDATHF.
 
Authors :  S. Connelly, K. Demartino, D. L. Boger, I. A. Wilson
Date :  26 Apr 12  (Deposition) - 31 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Connelly, J. K. Demartino, D. L. Boger, I. A. Wilson
Biological And Structural Evaluation Of 10R- And 10S-Methylthio-Ddacthf Reveals A New Role For Sulfur In Inhibition Of Glycinamide Ribonucleotide Transformylase.
Biochemistry V. 52 5133 2013
PubMed-ID: 23869564  |  Reference-DOI: 10.1021/BI4005182

(-) Compounds

Molecule 1 - TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3
    Chains: A
    EC Number: 6.3.4.13, 6.3.3.1, 2.1.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 808-1010
    Gene: GART, PGFT, PRGS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PHOSPHORIBOSYLAMINE--GLYCINE LIGASE, GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, GARS, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE, PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE, AIR SYNTHASE, AIRS, PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE, 5'- PHOSPHORIBOSYLGLYCINAMIDE TRANSFORMYLASE, GAR TRANSFORMYLASE, GART

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DXZ1Ligand/IonN-({4-[(1R)-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDROPYRIMIDIN-5-YL)-1-(METHYLSULFANYL)BUTYL]PHENYL}CARBONYL)-L-GLUTAMIC ACID
2PO41Ligand/IonPHOSPHATE ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1DXZ1Ligand/IonN-({4-[(1R)-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDROPYRIMIDIN-5-YL)-1-(METHYLSULFANYL)BUTYL]PHENYL}CARBONYL)-L-GLUTAMIC ACID
2PO41Ligand/IonPHOSPHATE ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1DXZ2Ligand/IonN-({4-[(1R)-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDROPYRIMIDIN-5-YL)-1-(METHYLSULFANYL)BUTYL]PHENYL}CARBONYL)-L-GLUTAMIC ACID
2PO42Ligand/IonPHOSPHATE ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , ASN A:13 , LEU A:14 , GLN A:15 , ALA A:16 , LYS A:45 , HIS A:174 , HOH A:498 , HOH A:502 , HOH A:515 , HOH A:532BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWARELYS A:157 , ARG A:168 , HOH A:423BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASN A:119 , ALA A:120 , HIS A:121 , GLU A:122 , VAL A:162 , SER A:166 , HOH A:528BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:64 , PHE A:88 , MET A:89 , ARG A:90 , ILE A:91 , LEU A:92 , VAL A:97 , ALA A:140 , GLU A:141 , VAL A:143 , HOH A:435 , HOH A:437 , HOH A:509BINDING SITE FOR RESIDUE DXZ A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EW3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EW3)

(-) Exons   (0, 0)

(no "Exon" information available for 4EW3)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains d4ew3a_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhh......eeeeeee....hhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeeee......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ew3 A   1 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHH 205
                                    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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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EW3)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)

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  4ew3
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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR2_HUMAN | P22102: 1mej 1men 1meo 1njs 1rbm 1rbq 1rby 1rbz 1rc0 1rc1 1zlx 1zly 2qk4 2v9y 4ew1 4ew2 4zyt 4zyu 4zyv 4zyw 4zyx 4zyy 4zyz 4zz0 4zz1 4zz2 4zz3 5j9f

(-) Related Entries Specified in the PDB File

1njs HUMAN GAR TFASE IN COMPLEX WITH HYDROLYZED FORM OF 10- TRIFLUOROACETYL-5,10-DIDEAZA-ACYCLIC-5,6,7,8- TETRAHYDROFOLIC ACID
4ew1
4ew2