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(-) Description

Title :  CRYSTAL STRUCTURE OF GAR SYNTHETASE FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  S. Baba, M. Kanagawa, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 09 Oct 07  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycinamide Ribonucleotide Synthetase, Gar Synthetase, Atp Binding, Purine Nucleotide Biosynthetic Pathway, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sampei, S. Baba, M. Kanagawa, H. Yanai, T. Ishii, H. Kawai, Y. Fukai, A. Ebihara, N. Nakagawa, G. Kawai
Crystal Structures Of Glycinamide Ribonucleotide Synthetase Purd, From Thermophilic Eubacteria
J. Biochem. V. 148 429 2010
PubMed-ID: 20716513  |  Reference-DOI: 10.1093/JB/MVQ088

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE
    Chains: A
    EC Number: 6.3.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-HISTEV
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 1462
    Synonym: GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:212 , LYS A:214 , GLY A:226 , TYR A:269 , ASN A:285 , ARG A:287 , HOH A:651 , HOH A:669 , HOH A:694BINDING SITE FOR RESIDUE PO4 A 646

(-) SS Bonds  (0, 0)

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

(-) 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 2YRW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YRW)

(-) Exons   (0, 0)

(no "Exon" information available for 2YRW)

(-) 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:413
 aligned with Q5L3C7_GEOKA | Q5L3C7 from UniProtKB/TrEMBL  Length:430

    Alignment length:419
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
         Q5L3C7_GEOKA     - -MNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAELVHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPSQRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIKADGLAAGKGVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMAFVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALEAILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVLPRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIRGLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQLAAIDCDGLFYRRDIGRRAIE 418
               SCOP domains d2yrwa1 A:-1-101 automated matches                                                                    d2yrwa2 A:102-322 automated matches                                                                                                                                                                                          d2yrwa3 A:323-418 automated matches                                                              SCOP domains
               CATH domains --2yrwA01 A:2-93  [code=3.40.50.20, no name defined]                                          -------------------------2yrwA02 A:119-188 ATP-grasp       fold, A domain                      2yrwA03 A:189-324 ATP-grasp fold, B domain                                                                                              2yrwA04 A:325-418 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4                     CATH domains
               Pfam domains -GARS_N-2yrwA03 A:1-100                                                                              GARS_A-2yrwA01 A:101-293                                                                                                                                                                         -------------------------------GARS_C-2yrwA02 A:325-417                                                                     - Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhh....eeeeeeee...hhhhh.ee......hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee.------.eeee.hhhhhhhhhhhhhhhh........eeeee....eeeeeeeeee..eeee....ee..eee...eeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh..hhhhhhhhhhh...........eeeeeeeee...........ee.hhhhh....eeee..eeee..eeee...eeeeeeeee.hhhhhhhhhhhhhh......ee.....hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yrw A  -1 HMNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAELVHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPSQRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIKAD------GVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMAFVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALEAILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVLPRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIRGLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQLAAIDCDGLFYRRDIGRRAIE 418
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139     |   -  |    159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
                            ||                                                                                                                                             145    152                                                                                                                                                                                                                                                                          
                           -1|                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             1
   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, 3)

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  (4, 4)

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

(-) 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   (Q5L3C7_GEOKA | Q5L3C7)
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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        Q5L3C7_GEOKA | Q5L3C7: 2yrx 2ys6 2ys7

(-) Related Entries Specified in the PDB File

1gso GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E.COLI
2yrx RELATED ID: GKA001000268.1 RELATED DB: TARGETDB