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(-) Description

Title :  SAICAR SYNTHETASE COMPLEXED WITH CAIR-MG2+ AND ADP
 
Authors :  N. D. Ginder, R. B. Honzatko
Date :  21 Apr 06  (Deposition) - 16 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Purc, Ade2, Ade1, Nucleotide Complex, Magnesium Coordination, Metal Coordination, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. D. Ginder, D. J. Binkowski, H. J. Fromm, R. B. Honzatko
Nucleotide Complexes Of Escherichia Coli Phosphoribosylaminoimidazole Succinocarboxamide Synthetase.
J. Biol. Chem. V. 281 20680 2006
PubMed-ID: 16687397  |  Reference-DOI: 10.1074/JBC.M602109200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A, B
    EC Number: 6.3.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PURC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SAICAR SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2C2R2Ligand/Ion5-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXYLIC ACID
3FMT2Ligand/IonFORMIC ACID
4MG6Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREADP A:238 , FMT A:243 , HOH A:244 , HOH A:245 , HOH A:246BINDING SITE FOR RESIDUE MG A 239
02AC2SOFTWAREGLU A:90 , ASP A:129 , MG A:241 , C2R A:242 , HOH A:248 , HOH A:249BINDING SITE FOR RESIDUE MG A 240
03AC3SOFTWAREGLU A:90 , ASP A:129 , MG A:240 , C2R A:242 , FMT A:243 , HOH A:250 , HOH A:251BINDING SITE FOR RESIDUE MG A 241
04AC4SOFTWAREADP B:238 , FMT B:243 , HOH B:244 , HOH B:245 , HOH B:246BINDING SITE FOR RESIDUE MG B 239
05AC5SOFTWAREGLU B:90 , ASP B:129 , MG B:241 , C2R B:242 , HOH B:248 , HOH B:249BINDING SITE FOR RESIDUE MG B 240
06AC6SOFTWAREGLU B:90 , ASP B:129 , MG B:240 , C2R B:242 , FMT B:243 , HOH B:250 , HOH B:251BINDING SITE FOR RESIDUE MG B 241
07AC7SOFTWARETYR A:8 , GLY A:10 , LYS A:11 , ALA A:12 , LYS A:13 , VAL A:15 , LEU A:24 , GLN A:69 , LYS A:82 , LEU A:84 , MET A:86 , LYS A:123 , GLU A:179 , ASP A:191 , MG A:239 , FMT A:243 , HOH A:245 , HOH A:246 , HOH A:291 , HOH A:311 , HOH A:328BINDING SITE FOR RESIDUE ADP A 238
08AC8SOFTWAREASP A:36 , GLU A:90 , ARG A:94 , GLY A:99 , SER A:100 , ASP A:129 , ASP A:175 , LYS A:177 , ASP A:196 , GLY A:197 , SER A:198 , ARG A:199 , ARG A:215 , MG A:240 , MG A:241 , FMT A:243 , HOH A:248 , HOH A:249 , HOH A:250 , HOH A:281BINDING SITE FOR RESIDUE C2R A 242
09AC9SOFTWARETYR B:8 , GLY B:10 , LYS B:11 , ALA B:12 , LYS B:13 , VAL B:15 , GLN B:69 , LYS B:82 , LEU B:84 , MET B:86 , LYS B:123 , GLU B:179 , ASP B:191 , MG B:239 , FMT B:243 , HOH B:244 , HOH B:246BINDING SITE FOR RESIDUE ADP B 238
10BC1SOFTWAREGLU B:90 , ARG B:94 , GLY B:99 , SER B:100 , ASP B:129 , ASP B:175 , LYS B:177 , ASP B:196 , GLY B:197 , SER B:198 , ARG B:199 , ARG B:215 , MG B:240 , MG B:241 , FMT B:243 , HOH B:248 , HOH B:250 , HOH B:264 , HOH B:275 , HOH B:319BINDING SITE FOR RESIDUE C2R B 242
11BC2SOFTWARELYS A:11 , GLU A:90 , LYS A:123 , LYS A:177 , GLU A:179 , ADP A:238 , MG A:239 , MG A:241 , C2R A:242 , HOH A:244 , HOH A:246BINDING SITE FOR RESIDUE FMT A 243
12BC3SOFTWARELYS B:11 , GLU B:90 , LYS B:123 , LYS B:177 , GLU B:179 , ADP B:238 , MG B:239 , MG B:241 , C2R B:242 , HOH B:246 , HOH B:251BINDING SITE FOR RESIDUE FMT B 243

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:114 -Pro A:115
2Asn B:114 -Pro B:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_ECOLI86-100
 		  2A:86-100
B:86-100
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_ECOLI173-181
 		  2A:173-181
B:173-181

(-) Exons   (0, 0)

(no "Exon" information available for 2GQS)

(-) 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:237
 aligned with PUR7_ECOLI | P0A7D7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           PUR7_ECOLI     1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
               SCOP domains d2gqsa_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------2gqsA02 A:85-220 ATP-grasp fold, B domain                                                                                               ----------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee.....eeeeee..eeeehhhheeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhhhh.....eeeeeeeeeee.hhhhh..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eeee..eeee....hhh.eeeee........hhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqs A   1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with PUR7_ECOLI | P0A7D7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           PUR7_ECOLI     1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
               SCOP domains d2gqsb_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------2gqsB02 B:85-220 ATP-grasp fold, B domain                                                                                               ----------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeee......eeeeee..eeeehhhheeee..hhhhhhhhhhhhhhhhhhh......eeee....eeeee..ee..eeeeeeee.hhhhhhhhh.....eeeeeeeeeee.hhhhh..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eeee..eeee........eeeee........hhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqs B   1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GQS)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PUR7_ECOLI | P0A7D7)
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:0004638    phosphoribosylaminoimidazole carboxylase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).
    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:0046084    adenine biosynthetic process    The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR7_ECOLI | P0A7D7: 2gqr

(-) Related Entries Specified in the PDB File

1a48 1kut 1obd 1obg 2gqr