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(-) Description

Title :  NUCLEOTIDE-BOUND STRUCTURES OF BACILLUS SUBTILIS GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE
 
Authors :  J. A. Bertrand, S. Chen, H. Zalkin, J. L. Smith
Date :  29 Apr 10  (Deposition) - 23 Mar 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Gar-Syn, Atp-Grasp, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Bertrand, S. Chen, H. Zalkin, J. L. Smith
Nucleotide-Bound Structures Of Bacillus Subtilis Glycinamid Ribonucleotide Synthetase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINE--GLYCINE LIGASE
    Chains: A
    EC Number: 6.3.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE, GARS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:103 , VAL A:141 , LYS A:143 , GLY A:150 , VAL A:153 , GLU A:185 , GLU A:186 , LEU A:188 , GLU A:192 , LYS A:214 , MET A:273 , ILE A:282 , GLU A:283 , MG A:451 , MG A:453 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE ADP A 461
2AC2SOFTWAREGLU A:283 , ASN A:285 , ADP A:461 , HOH A:2070BINDING SITE FOR RESIDUE MG A 451
3AC3SOFTWAREHIS A:167 , ASP A:172 , HOH A:2038BINDING SITE FOR RESIDUE MG A 452
4AC4SOFTWARELYS A:214 , GLU A:283 , ADP A:461BINDING SITE FOR RESIDUE MG A 453

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XD4)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Pro A:32
2Ala A:138 -Pro A:139
3Ser A:232 -Pro A:233
4Asp A:290 -Pro A:291
5Tyr A:336 -Pro A:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XD4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARSPS00184 Phosphoribosylglycinamide synthetase signature.PUR2_BACSU287-294  1A:287-294

(-) Exons   (0, 0)

(no "Exon" information available for 2XD4)

(-) 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:422
 aligned with PUR2_BACSU | P12039 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420  
           PUR2_BACSU     1 MNVLIIGKGGREHTLAWKAAQSSLVENVFAAPGNDGMAASAQLVNIEESDHAGLVSFAKQNQVGLTIVGPEVPLIEGLVDEFEKAGLHVFGPSKAAAIIEGSKQFAKDLMKKYDIPTAEYETFTSFDEAKAYVQEKGAPIVIKADGLAAGKGVTVAMTEEEAIACLHDFLEDEKFGDASASVVIEEYLSGEEFSLMAFVKGEKVYPMVIAQDHKRAFDGDKGPNTGGMGAYSPVPQISEETVRHAVETIVKPAAKAMVQEGRSFTGVLYAGLMLTENGSKVIEFNARFGDPETQVVLPRMESDLVQVLLDLLDDKEVDLRWKDTAAVSVVLASEGYPESYAKGTPIGSLAAETEQVVVFHAGTKAEGGEFVTNGGRVANVTAFDETFEAARDRVYKAVDEIFKPGLFFRKDIGARALKAAQK 422
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains GARS_N-2xd4A03 A:1-100                                                                              GARS_A-2xd4A01 A:101-293                                                                                                                                                                         -------------------------------GARS_C-2xd4A02 A:325-417                                                                     ----- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhh.....eeeeee.hhhhh...ee......hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee..hhhhh.eeee.hhhhhhhhhhhhh...........eeeee....eeeeeeeeee..eeee....ee..eee...eeee....eeee.....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..eeeeeeee.....hhhhhhh.....hhhhhhhhhhh...........eeeeeeeee...........eee........eeeee..eee....eee...eeeeeeeee.hhhhhhhhhhhhhhhhh...ee.....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xd4 A   1 MNVLIIGKGGREHTLAWKAAQSSLVENVFAAPGNDGMAASAQLVNIEESDHAGLVSFAKQNQVGLTIVGPEVPLIEGLVDEFEKAGLHVFGPSKAAAIIEGSKQFAKDLMKKYDIPTAEYETFTSFDEAKAYVQEKGAPIVIKADGLAAGKGVTVAMTEEEAIACLHDFLEDEKFGDASASVVIEEYLSGEEFSLMAFVKGEKVYPMVIAQDHKRAFDGDKGPNTGGMGAYSPVPQISEETVRHAVETIVKPAAKAMVQEGRSFTGVLYAGLMLTENGSKVIEFNARFGDPETQVVLPRMESDLVQVLLDLLDDKEVDLRWKDTAAVSVVLASEGYPESYAKGTPIGSLAAETEQVVVFHAGTKAEGGEFVTNGGRVANVTAFDETFEAARDRVYKAVDEIFKPGLFFRKDIGARALKAAQK 422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   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  (0, 0)

(no "SCOP Domain" information available for 2XD4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XD4)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: GARS_C] (12)
(-)
Clan: no clan defined [family: GARS_N] (12)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR2_BACSU | P12039)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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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 Related Entries

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        PUR2_BACSU | P12039: 2xcl

(-) Related Entries Specified in the PDB File

2xcl NUCLEOTIDE-BOUND STRUCTURES OF BACILLUS SUBTILIS GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE