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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE FROM CLOSTRIDIUM PERFRINGENS
 
Authors :  Y. Kim, R. Mulligan, K. Kwon, W. F. Anderson, A. Joachimiak
Date :  06 Jul 10  (Deposition) - 25 Aug 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Structure, Csgid, Ligase, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, R. Mulligan, K. Kwon, W. F. Anderson, A. Joachimiak
Crystal Structure Of Phosphoribosylaminoimidazole-Succinocarboxamide Synthase From Clostridium Perfringens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A, B
    EC Number: 6.3.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CPF_0673, PURC
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 195103
    Strain: ATCC 13124
    Synonym: SAICAR SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3CIT2Ligand/IonCITRIC ACID
4GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:9 , GLY A:11 , LYS A:12 , ALA A:13 , LYS A:14 , ILE A:16 , HIS A:70 , LYS A:83 , VAL A:85 , ILE A:87 , LYS A:124 , GLU A:180 , ASP A:192 , GOL A:244 , HOH A:550 , HOH A:623 , HOH A:656 , HOH A:705 , HOH A:707 , HOH A:843BINDING SITE FOR RESIDUE ADP A 241
2AC2SOFTWAREGLU A:91 , ARG A:95 , GLY A:100 , SER A:101 , ASP A:176 , LYS A:178 , ASP A:197 , THR A:198 , CYS A:199 , ARG A:200 , ARG A:216 , CIT A:243 , HOH A:530 , HOH A:542 , HOH A:599 , HOH A:663 , HOH A:664 , HOH A:743 , HOH A:853 , HOH A:855BINDING SITE FOR RESIDUE AMP A 242
3AC3SOFTWARELYS A:12 , THR A:34 , ALA A:35 , PHE A:36 , LYS A:212 , ARG A:216 , AMP A:242 , HOH A:725 , HOH A:743 , HOH A:808 , HOH A:816BINDING SITE FOR RESIDUE CIT A 243
4AC4SOFTWARETYR A:9 , ADP A:241 , HOH A:563 , HOH A:611BINDING SITE FOR RESIDUE GOL A 244
5AC5SOFTWARETYR B:9 , GLY B:11 , LYS B:12 , ALA B:13 , LYS B:14 , ILE B:16 , HIS B:70 , LYS B:83 , VAL B:85 , ILE B:87 , LYS B:124 , GLU B:180 , ASP B:192 , HOH B:584 , HOH B:624 , HOH B:634 , HOH B:698 , HOH B:702 , HOH B:715 , HOH B:730BINDING SITE FOR RESIDUE ADP B 241
6AC6SOFTWAREGLU B:91 , ARG B:95 , GLY B:100 , SER B:101 , ASP B:176 , LYS B:178 , ASP B:197 , THR B:198 , CYS B:199 , ARG B:200 , ARG B:216 , CIT B:243 , HOH B:531 , HOH B:565 , HOH B:600 , HOH B:642 , HOH B:756 , HOH B:791 , HOH B:794 , HOH B:827 , HOH B:828BINDING SITE FOR RESIDUE ADP B 242
7AC7SOFTWARELYS B:12 , THR B:34 , ALA B:35 , PHE B:36 , LYS B:212 , ARG B:216 , ADP B:242 , HOH B:565 , HOH B:591 , HOH B:791BINDING SITE FOR RESIDUE CIT B 243

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_CLOP187-101
 		  2A:87-101
B:87-101
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_CLOP1174-182
 		  2A:174-182
B:174-182

(-) Exons   (0, 0)

(no "Exon" information available for 3NUA)

(-) 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:236
 aligned with PUR7_CLOP1 | Q0TTB4 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:236
                             1                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229      
           PUR7_CLOP1     - -MVNQLEMLYEGKAKKIYATDKEDMVIVHYKDDATAFNGEKKAQIESKGVLNNEITSLIFEMLNKEGIKTHFVEKLNDRDQLCKKVEIVPLEVIVRNVAAGSMAKRLGLEEGYELKTTVFELSYKDDSLGDPLINDYHAVGIGATTFEELNKIYEITAKVNEILKEAFKKQNINLIDFKLEFGRYNGEILLADEISPDTCRFWDATTGEKMDKDRFRRDMGNVINGYREVLNRLRN 235
               SCOP domains d3nuaa_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeeeehhhhhhhhh....eeeeeeeeeeee.hhhhh..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeee.......eeeee........hhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY----------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nua A   0 AMVNQLEMLYEGKAKKIYATDKEDMVIVHYKDDATAFNGEKKAQIESKGVLNNEITSLIFEMLNKEGIKTHFVEKLNDRDQLCKKVEIVPLEVIVRNVAAGSMAKRLGLEEGYELKTTVFELSYKDDSLGDPLINDYHAVGIGATTFEELNKIYEITAKVNEILKEAFKKQNINLIDFKLEFGRYNGEILLADEISPDTCRFWDATTGEKMDKDRFRRDMGNVINGYREVLNRLRN 235
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229      


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with PUR7_CLOP1 | Q0TTB4 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:237
                              1                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       
           PUR7_CLOP1     - --MVNQLEMLYEGKAKKIYATDKEDMVIVHYKDDATAFNGEKKAQIESKGVLNNEITSLIFEMLNKEGIKTHFVEKLNDRDQLCKKVEIVPLEVIVRNVAAGSMAKRLGLEEGYELKTTVFELSYKDDSLGDPLINDYHAVGIGATTFEELNKIYEITAKVNEILKEAFKKQNINLIDFKLEFGRYNGEILLADEISPDTCRFWDATTGEKMDKDRFRRDMGNVINGYREVLNRLRN 235
               SCOP domains d3nuab_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SAICAR_synt-3nuaB01 B:4-235                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) -----SAICAR_synt-3nuaB02 B:4-235                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author .....eeeeeee...eeeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeeeehhhhhhhh.....eeeeeeeeeeee.hhhhh..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeee.......eeeee........hhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY----------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nua B  -1 NAMVNQLEMLYEGKAKKIYATDKEDMVIVHYKDDATAFNGEKKAQIESKGVLNNEITSLIFEMLNKEGIKTHFVEKLNDRDQLCKKVEIVPLEVIVRNVAAGSMAKRLGLEEGYELKTTVFELSYKDDSLGDPLINDYHAVGIGATTFEELNKIYEITAKVNEILKEAFKKQNINLIDFKLEFGRYNGEILLADEISPDTCRFWDATTGEKMDKDRFRRDMGNVINGYREVLNRLRN 235
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SAICAR_synt] (7)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PUR7_CLOP1 | Q0TTB4)
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:0004639    phosphoribosylaminoimidazolesuccinocarboxamide synthase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + 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.

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