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(-) Description

Title :  PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE FROM VIBRIO CHOLERAE
 
Authors :  J. Osipiuk, M. Zhou, L. Papazisi, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  06 Oct 10  (Deposition) - 20 Oct 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Phosphoribosylaminoimidazole Synthetase, Purm, Amp, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, L. Papazisi, W. F. Anderson, A. Joachimiak
Phosphoribosylformylglycinamidine Cyclo-Ligase From Vibrio Cholerae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
    Chains: A
    EC Number: 6.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PURM, VC2226, VC_2226
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: O1 BIOVAR EL TOR STR. N16961
    Synonym: AIRS, PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE, AIR SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2CIT1Ligand/IonCITRIC ACID
3EDO1Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2CIT2Ligand/IonCITRIC ACID
3EDO2Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:24 , ASP A:108 , ILE A:124 , GLY A:140 , GLY A:141 , GLU A:142 , THR A:143 , HOH A:523 , HOH A:606 , HOH A:607 , HOH A:608 , HOH A:609 , HOH A:610BINDING SITE FOR RESIDUE AMP A 501
2AC2SOFTWARELYS A:80 , ASP A:82 , LEU A:213 , TRP A:282 , GLU A:285 , HOH A:432 , HOH A:497 , HOH A:624BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREASN A:193 , GLY A:194 , TYR A:195 , SER A:196 , LEU A:197 , GLY A:250 , HOH A:360 , HOH A:535 , HOH A:536 , HOH A:599 , HOH A:600BINDING SITE FOR RESIDUE CIT A 503
4AC4SOFTWAREVAL A:98 , ILE A:171 , ALA A:244 , ILE A:245BINDING SITE FOR RESIDUE EDO A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P4E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P4E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P4E)

(-) Exons   (0, 0)

(no "Exon" information available for 3P4E)

(-) 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:323
 aligned with PUR5_VIBCH | Q9KPY6 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:329
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337         
           PUR5_VIBCH    18 DAGNALVERIKGAVKRTRRPEVMGGLGGFGALCELPTKYKHPVLVSGTDGVGTKLRLALDMKKHDTIGIDLVAMCVNDLIVQGAEPLFFLDYYATGKLDVDTAAEVISGIADGCLQAGCALIGGETAEMPGMYEGEDYDVAGFCVGVVEKEEIIDGSKVQVGDALIAVGSSGPHSNGYSLVRKILEVSKADKNERLAGKTIGEHLLAPTKIYIKSGLKLIAEHDIHAISHITGGGFWENIPRVLPEGTKAVIDGKSWEWPVIFQWLQEKGNVTTHEMYRTFNCGVGLIIALPKDQANAAVALLQAEGETAWVIGEIAAANSNEAQVEIN 346
               SCOP domains d3p4ea1 A:18-171 automat      ed matches                                                                                                                  d3p4ea2 A:172-346 automated matches                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------AIRS-3p4eA01 A      :28-143                                                                                         ---------------------------------AIRS_C-3p4eA02 A:177-344                                                                                                                                                -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....ee.------.ee........eeeeeeee..hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh.eeeeeeeee.........eeeeeeeeeeee.hhh..........eeeeee.......hhhhhhhhhhhhh.....ee..eehhhhhhh....hhhhhhhhhhhh...eeee...hhhhhhhhhhh...eeeeee......hhhhhhhhhhhh.hhhhhhh.....eeeeeeehhhhhhhhhhhhhhh...eeeeeeeee.......eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p4e A  18 DAGNALVERIKGAVKRTRRPEVMG------ALCELPTKYKHPVLVSGTDGVGTKLRLALDMKKHDTIGIDLVAMCVNDLIVQGAEPLFFLDYYATGKLDVDTAAEVISGIADGCLQAGCALIGGETAEMPGMYEGEDYDVAGFCVGVVEKEEIIDGSKVQVGDALIAVGSSGPHSNGYSLVRKILEVSKADKNERLAGKTIGEHLLAPTKIYIKSGLKLIAEHDIHAISHITGGGFWENIPRVLPEGTKAVIDGKSWEWPVIFQWLQEKGNVTTHEMYRTFNCGVGLIIALPKDQANAAVALLQAEGETAWVIGEIAAANSNEAQVEIN 346
                                    27        37   |     -|       57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337         
                                                  41     48
   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)
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P4E)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PUR5_VIBCH | Q9KPY6)
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.
    GO:0009152    purine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a 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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