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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE SYNTHETASE FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha And Beta Proteins, Ligase, Purine Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Baba, Y. Watanabe, N. Nakagawa, A. Ebihara, S. Kuramitsu, S. Yokoyama, G. Sampei, G. Kawai
Crystal Structures And Ligand Binding Of Purm Proteins From Thermus Thermophilus And Geobacillus Kaustophilus
J. Biochem. 2015
PubMed-ID: 26515187  |  Reference-DOI: 10.1093/JB/MVV107

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
    Chains: A
    EC Number: 6.3.3.1
    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: AIRS, PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE, AIR SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z01)

(-) Sites  (0, 0)

(no "Site" information available for 2Z01)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z01)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:211 -Pro A:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z01)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z01)

(-) Sequences/Alignments

Asymmetric 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:313
 aligned with PUR5_GEOKA | Q5L3D0 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:326
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      
           PUR5_GEOKA    17 QAVALMKEHVQKTMRPEVLGGIGGFGGLFDLSALGYRQPVLISGTDGVGTKLKLAFLLDRHDTIGIDCVAMCVNDIIVQGAEPLFFLDYIACGKAVPEKIAAIVKGVADGCVEAGCALIGGETAEMPGMYDEDEYDLAGFAVGVAEKERLITGETIQAGDALVGLPSSGLHSNGYSLVRRIVFEQAKLSLDEIYEPLDVPLGEELLKPTRIYAKLLRSVRERFTIKGMAHITGGGLIENIPRMLPPGIGARIQLGSWPILPIFDFLREKGSLEEEEMFSVFNMGIGLVLAVSPETAAPLVEWLSERGEPAYIIGEVAKGAGVSFAG 342
               SCOP domains d2z01a1 A:17-167 aut     omated matches                                                                                                                d2z01a2 A:168-342 automated matches                                                                                                                                             SCOP domains
               CATH domains 2z01A01 A:17-167  [c     ode=3.30.1330.10, no name defined]                                                                                            2z01A02 A:168-342 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                                   CATH domains
               Pfam domains AIRS-2z01A01 A:17-13     9                                                                                                 --        -----------------------AIRS_C-2z01A02 A:173-341                                                                                                                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...ee.-----..ee.hhhhh...eeeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh.eeee..ee.--------.eeeeeeeeeeee.hhh..........eeeeee.......hhhhhhhhhhh...............hhhhhhhh....hhhhhhhhhhhh...eeee...hhhhhhhhhhh...eeeeee......hhhhhhhhhhh..hhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh....eeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z01 A  17 QAVALMKEHVQKTMRPEVLG-----GGLFDLSALGYRQPVLISGTDGVGTKLKLAFLLDRHDTIGIDCVAMCVNDIIVQGAEPLFFLDYIACGKAVPEKIAAIVKGVADGCVEAGCALIGGETAE--------EYDLAGFAVGVAEKERLITGETIQAGDALVGLPSSGLHSNGYSLVRRIVFEQAKLSLDEIYEPLDVPLGEELLKPTRIYAKLLRSVRERFTIKGMAHITGGGLIENIPRMLPPGIGARIQLGSWPILPIFDFLREKGSLEEEEMFSVFNMGIGLVLAVSPETAAPLVEWLSERGEPAYIIGEVAKGAGVSFAG 342
                                    26        36     |  46        56        66        76        86        96       106       116       126       136    |    -   |   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      
                                              36    42                                                                                                141      150
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: AIRS] (11)
(-)
Clan: no clan defined [family: AIRS_C] (13)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PUR5_GEOKA | Q5L3D0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0004641    phosphoribosylformylglycinamidine cyclo-ligase activity    Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + 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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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