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(-) Description

Title :  STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG AND AMPPNP
 
Authors :  J. B. Thoden, S. Firestine, A. Nixon, S. J. Benkovic, H. M. Holden
Date :  09 May 00  (Deposition) - 02 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transformylase, Purine Biosynthesis, Atp-Grasp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, S. Firestine, A. Nixon, S. J. Benkovic, H. M. Holden
Molecular Structure Of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase.
Biochemistry V. 39 8791 2000
PubMed-ID: 10913290  |  Reference-DOI: 10.1021/BI000926J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE 2
    Chains: A, B
    EC Number: 2.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CL1Ligand/IonCHLORIDE ION
3MG5Ligand/IonMAGNESIUM ION
4MPO1Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5NA2Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:279 , ANP A:400 , HOH A:1119 , HOH A:1131BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREGLU A:267 , GLU A:279 , ANP A:400 , HOH A:1113BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWAREASP A:286 , ANP A:400 , HOH A:1143 , HOH A:1258 , HOH A:1792 , HOH A:1794BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWAREGLU B:279 , ANP B:961 , HOH B:1615 , HOH B:1885BINDING SITE FOR RESIDUE MG B 401
05AC5SOFTWAREGLU B:267 , GLU B:279 , ANP B:961 , HOH B:1473BINDING SITE FOR RESIDUE MG B 402
06AC6SOFTWAREALA A:53 , HOH A:1288 , HIS B:51 , ALA B:53 , HOH B:1563 , HOH B:2078BINDING SITE FOR RESIDUE NA B 960
07AC7SOFTWAREASN A:100 , VAL A:101 , PRO A:103 , HOH A:1155 , HOH A:1162 , HOH A:1963BINDING SITE FOR RESIDUE NA A 961
08AC8SOFTWAREARG A:43 , VAL A:58 , ARG A:119 , PHE A:134BINDING SITE FOR RESIDUE CL A 970
09AC9SOFTWAREARG A:114 , ILE A:153 , LYS A:155 , SER A:160 , SER A:161 , GLY A:162 , GLN A:165 , GLU A:195 , GLY A:196 , VAL A:198 , PHE A:200 , GLU A:203 , GLU A:267 , PHE A:269 , GLU A:279 , MG A:401 , MG A:402 , MG A:403 , HOH A:1113 , HOH A:1119 , HOH A:1131 , HOH A:1138 , HOH A:1143 , HOH A:1158 , HOH A:1167 , HOH A:1175 , HOH A:1192 , HOH A:1252 , HOH A:1792BINDING SITE FOR RESIDUE ANP A 400
10BC1SOFTWAREARG B:114 , SER B:130 , LYS B:155 , SER B:159 , SER B:160 , SER B:161 , GLY B:162 , GLU B:195 , GLY B:196 , VAL B:198 , PHE B:200 , GLU B:203 , GLN B:225 , GLU B:267 , PHE B:269 , GLU B:279 , MG B:401 , MG B:402 , HOH B:1461 , HOH B:1473 , HOH B:1579 , HOH B:1615 , HOH B:1626 , HOH B:1636 , HOH B:1677 , HOH B:2063 , HOH B:2064BINDING SITE FOR RESIDUE ANP B 961
11BC2SOFTWAREASP A:46 , MET A:50 , HIS A:51 , ARG A:55 , SER A:56 , GLU A:143 , HOH A:1209 , HOH A:1293 , HOH A:1342 , HOH A:1952 , LEU B:8 , HIS B:54BINDING SITE FOR RESIDUE MPO A 950

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Val A:102 -Pro A:103
2Tyr A:150 -Pro A:151
3Gln A:235 -Pro A:236
4Val B:102 -Pro B:103
5Tyr B:150 -Pro B:151
6Gln B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EYZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1EYZ)

(-) 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:389
 aligned with PURT_ECOLI | P33221 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           PURT_ECOLI     2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
               SCOP domains d1eyza2 A:2-112 Glycinamide ribonucleotide transformylase PurT, N-domain                                       d1eyza3 A:113-318 Glycinamide ribonucleotide transformylase PurT, domain 2                                                                                                                                    d1eyza1 A:319-392 Glycinamide ribonucleotide transformylase PurT, C-domain SCOP domains
               CATH domains 1eyzA01 A:2-122  [code=3.40.50.20, no name defined]                                                                      1eyzA02 A:123-196 ATP-grasp fold, A domain                                1eyzA03 A:197-391 ATP-grasp fold, B domain                                                                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..hhhhhhhhhhhhh...eeeeee....hhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhhh...--..eeeee.....eeeeeeeeee..eeee...eeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeee..eeee...eeehhhhh....eeeee.....eeee...eeeeee..hhhhhhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyz A   2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRA--GRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                                                                                                                                   187  |                                                                                                                                                                                                          
                                                                                                                                                                                                                      190                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with PURT_ECOLI | P33221 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           PURT_ECOLI     2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRAGAGRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
               SCOP domains d1eyzb2 B:2-112 Glycinamide ribonucleotide transformylase PurT, N-domain                                       d1eyzb3 B:113-318 Glycinamide ribonucleotide transformylase PurT, domain 2                                                                                                                                    d1eyzb1 B:319-392 Glycinamide ribonucleotide transformylase PurT, C-domain SCOP domains
               CATH domains 1eyzB01 B:2-122  [code=3.40.50.20, no name defined]                                                                      1eyzB02 B:123-196 ATP-grasp fold, A domain                                1eyzB03 B:197-391 ATP-grasp fold, B domain                                                                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhh..eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhh......--..eeeee.....eeeeeeeeee..eeee...eeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeee..eeee...eeehhhhh....eeeee.....eeee...eeeeee..hhhhhhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eyz B   2 TLLGTALRPAATRVMLLGSGELGKEVAIECQRLGVEVIAVDRYADAPAMHVAHRSHVINMLDGDALRRVVELEKPHYIVPEIEAIATDMLIQLEEEGLNVVPCARATKLTMNREGIRRLAAEELQLPTSTYRFADSESLFREAVADIGYPCIVKPVMSSSGKGQTFIRSAEQLAQAWKYAQQGGRA--GRVIVEGVVKFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSPLALERAQEIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGGIRQYGPAASAVILPQLTSQNVTFDNVQNAVGADLQIRLFGKPEIDGSRRLGVALATAESVVDAIERAKHAAGQVKVQG 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                                                                                                                                   187  |                                                                                                                                                                                                          
                                                                                                                                                                                                                      190
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EYZ)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PURT_ECOLI | P33221)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008776    acetate kinase activity    Catalysis of the reaction: ATP + acetate = ADP + acetyl phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0004638    phosphoribosylaminoimidazole carboxylase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).
    GO:0004639    phosphoribosylaminoimidazolesuccinocarboxamide synthase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate.
    GO:0043815    phosphoribosylglycinamide formyltransferase 2 activity    Catalysis of the reaction: formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + diphosphate.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0046084    adenine biosynthetic process    The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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.
    GO:0009152    purine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a 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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  1eyz
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  PURT_ECOLI | P33221
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 Related Entries

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

UniProtKB/Swiss-Prot
        PURT_ECOLI | P33221: 1ez1 1kj8 1kj9 1kji 1kjj 1kjq 1nfe

(-) Related Entries Specified in the PDB File

1ez1 1EZ1 CONTAINS THE SAME PROTEIN COMPLEXED WITH GLYCINAMIDE RIBONUCLEOTIDE.