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(-) Description

Title :  GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI.
 
Authors :  W. Wang, T. J. Kappock, J. Stubbe, S. E. Ealick
Date :  08 Sep 98  (Deposition) - 09 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Gar-Syn, Glycinamide Ribonucleotide Synthetase, Atp-Grasp, Purine De Novo Biosynthetic Pathway, Substrate Channeling, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Wang, T. J. Kappock, J. Stubbe, S. E. Ealick
X-Ray Crystal Structure Of Glycinamide Ribonucleotide Synthetase From Escherichia Coli.
Biochemistry V. 37 15647 1998
PubMed-ID: 9843369  |  Reference-DOI: 10.1021/BI981405N
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE)
    Cell LineB834(DE3)
    ChainsA
    EC Number6.3.4.13
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainTX635
    SynonymPURD GEN PRODUCT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GSO)

(-) Sites  (0, 0)

(no "Site" information available for 1GSO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Pro A:32
2Ala A:140 -Pro A:141
3Ser A:234 -Pro A:235
4Tyr A:341 -Pro A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARSPS00184 Phosphoribosylglycinamide synthetase signature.PUR2_ECOLI290-297  1A:290-297

(-) Exons   (0, 0)

(no "Exon" information available for 1GSO)

(-) 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:419
 aligned with PUR2_ECOLI | P15640 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:428
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418        
           PUR2_ECOLI     - --MKVLVIGNGGREHALAWKAAQSPLVETVFVAPGNAGTALEPALQNVAIGVTDIPALLDFAQNEKIDLTIVGPEAPLVKGVVDTFRAAGLKIFGPTAGAAQLEGSKAFTKDFLARHKIPTAEYQNFTEVEPALAYLREKGAPIVIKADGLAAGKGVIVAMTLEEAEAAVHDMLAGNAFGDAGHRIVIEEFLDGEEASFIVMVDGEHVLPMATSQDHKRVGDKDTGPNTGGMGAYSPAPVVTDDVHQRTMERIIWPTVKGMAAEGNTYTGFLYAGLMIDKQGNPKVIEFNCRFGDPETQPIMLRMKSDLVELCLAACESKLDEKTSEWDERASLGVVMAAGGYPGDYRTGDVIHGLPLEEVAGGKVFHAGTKLADDEQVVTNGGRVLCVTALGHTVAEAQKRAYALMTDIHWDDCFCRKDIGWRAIER 426
               SCOP domains d1gsoa2 A:-2-103 Glycinamide ribonucleotide synthetase (GAR-syn), N-domain                               d1gsoa3 A:104-327 Glycinamide ribonucleotid      e synthetase (GAR-syn), domain 2                                                                                                                                               d1gsoa1 A:328-426 Glycinamide ribonucleotide    synthetase (GAR-syn), C-domain                      SCOP domains
               CATH domains ---1gsoA01 A:2-95  [code=3.40.50.20, no name defined]                                            -------------------------1gsoA02 A:121-190 ATP-gras      p fold, A domain                      1gsoA03 A:191-329 ATP-grasp fold, B domain                                                                                                 1gsoA04 A:330-425 Glycinamide Ribonucleotid   e Synthetase; Chain A, domain 4                   - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhh...eeeeeeee..hhhhh...eee.......hhhhhhhhhh....eeee..hhhhh..hhhhhhh...........hhhhhh.hhhhhhhhhh.......eeee....hhhhhhhhh...eeee.------..eeee..hhhhhhhhh..............eeeee...eeeeeeeeeee...eeeeeeeeee...............eeee......hhhhhhhhhh.hhhhhhhhhh.....eeeeeeeeeee....eeeeeee......hhhhhhhh....hhhhhhhhhh..hhh.........eeeeeee.........................eeee......---.......eeeeee.....hhhhhhhhhhhh...............hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gso A  -2 EFMKVLVIGNGGREHALAWKAAQSPLVETVFVAPGNAGTALEPALQNVAIGVTDIPALLDFAQNEKIDLTIVGPEAPLVKGVVDTFRAAGLKIFGPTAGAAQLEGSKAFTKDFLARHKIPTAEYQNFTEVEPALAYLREKGAPIVIKA------KGVIVAMTLEEAEAAVHDMLAGNAFGDAGHRIVIEEFLDGEEASFIVMVDGEHVLPMATSQDHKRVGDKDTGPNTGGMGAYSPAPVVTDDVHQRTMERIIWPTVKGMAAEGNTYTGFLYAGLMIDKQGNPKVIEFNCRFGDLETQPIMLRMKSDLVELCLAACESKLDEKTSEWDERASLGVVMAAGGYPGDYRTGDVIHGLPLEEVAGGKVFHAGTKLA---QVVTNGGRVLCVTALGHTVAEAQKRAYALMTDIHWDDCFCRKDIGWRAIER 426
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       | -    |  158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368   |   378       388       398       408       418        
                             ||                                                                                                                                              146    153                                                                                                                                                                                                                        372 376                                                  
                            -1|                                                                                                                                                                                                                                                                                                                                                                                                                                         
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                         

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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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR2_ECOLI | P15640)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) 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:0004637    phosphoribosylamine-glycine ligase activity    Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate.
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: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:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    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.

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  Cis Peptide Bonds
    Ala A:140 - Pro A:141   [ RasMol ]  
    Ala A:31 - Pro A:32   [ RasMol ]  
    Ser A:234 - Pro A:235   [ RasMol ]  
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