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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 :  1.90
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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:375 , ARG A:376 , HOH A:704 , HOH A:711BINDING SITE FOR RESIDUE PO4 A 600
2AC2SOFTWAREARG A:11 , ARG A:287 , ASP A:290 , ARG A:376 , HOH A:664 , HOH A:668 , HOH A:704BINDING SITE FOR RESIDUE PO4 A 601
3AC3SOFTWAREGLU A:186 , LEU A:188 , GLU A:192 , LYS A:214BINDING SITE FOR RESIDUE AMP A 500

(-) SS Bonds  (0, 0)

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

(-) 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 2YRX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YRX)

(-) 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:420
 aligned with Q5L3C7_GEOKA | Q5L3C7 from UniProtKB/TrEMBL  Length:430

    Alignment length:424
                                   1                                                                                                                                                                                                                                                                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413    
         Q5L3C7_GEOKA     - -------MNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAELVHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPSQRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIKADGLAAGKGVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMAFVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALEAILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVLPRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIRGLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQLAAIDCDGLFYRRDIGRRAI 417
               SCOP domains d2yrxa1 A:-7-101 automated matches                                                                          d2yrxa2 A:102-322 automated matches                                                                                                                                                                                          d2yrxa3 A:323-417 automated matches                                                             SCOP domains
               CATH domains --------2yrxA01 A:2-93  [code=3.40.50.20, no name defined]                                          -------------------------2yrxA02 A:119-188 ATP-grasp     fold, A domain                        2yrxA03 A:189-324 ATP-grasp fold, B domain                                                                                              2yrxA04 A:325-417 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4                    CATH domains
               Pfam domains -------GARS_N-2yrxA03 A:1-100                                                                              GARS_A-2yrxA01 A:101-293                                                                                                                                                                         -------------------------------GARS_C-2yrxA02 A:325-417                                                                      Pfam domains
         Sec.struct. author .......eeeeeee.hhhhhhhhhhhhh...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.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yrx A  -7 NLYFQSHMNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAELVHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPSQRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIKADG----KGVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMAFVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALEAILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVLPRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIRGLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQLAAIDCDGLFYRRDIGRRAI 417
                                  || 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143  |    153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413    
                                 -1|                                                                                                                                              146  151                                                                                                                                                                                                                                                                          
                                   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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 Related Entries

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

UniProtKB/TrEMBL
        Q5L3C7_GEOKA | Q5L3C7: 2yrw 2ys6 2ys7

(-) Related Entries Specified in the PDB File

2yrw GAR SYNTHETASE FROM GEOBACILLUS KAUSTOPHILUS RELATED ID: GKA001000268.2 RELATED DB: TARGETDB