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(-) Description

Title :  CRYSTAL STRUCTURE OF FAICAR SYNTHETASE (PURP) FROM M. JANNASCHII COMPLEXED WITH ATP AND AICAR
 
Authors :  Y. Zhang, R. H. White, S. E. Ealick
Date :  09 Sep 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Atp-Grasp Superfamily, Atp-Binding, Ligase, Magnesium, Manganese, Metal-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, R. H. White, S. E. Ealick
Crystal Structure And Function Of 5-Formaminoimidazole-4-Carboxamide Ribonucleotide Synthetase From Methanocaldococcus Jannaschii.
Biochemistry V. 47 205 2008
PubMed-ID: 18069798  |  Reference-DOI: 10.1021/BI701406G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5-FORMAMINOIMIDAZOLE-4-CARBOXAMIDE-1-(BETA)-D- RIBOFURANOSYL 5'-MONOPHOSPHATE SYNTHETASE
    Chains: A
    EC Number: 6.3.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: B834(DE3)
    Expression System Plasmid: PET19
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURP
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: 5-AMINOIMIDAZOLE-4-CARBOXAMIDE-1-BETA-D- RIBOFURANOSYL 5'-MONOPHOSPHATE-FORMATE LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1AMZ1Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL2Ligand/IonCHLORIDE ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1AMZ6Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
2ATP6Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:56 , ARG A:57BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREHIS A:27 , ARG A:314 , ASP A:316 , GLY A:317BINDING SITE FOR RESIDUE CL A 601
3AC3SOFTWAREHIS A:210 , ASP A:316 , THR A:319BINDING SITE FOR RESIDUE CL A 602
4AC4SOFTWAREPRO A:140 , ILE A:154 , LYS A:156 , TYR A:166 , GLU A:199 , GLU A:200 , TYR A:201 , ARG A:228 , GLU A:230 , ARG A:238 , TYR A:253 , ILE A:255 , GLN A:297 , LEU A:299 , PHE A:309 , GLU A:310 , HOH A:608 , HOH A:611 , HOH A:612 , HOH A:613 , HOH A:689 , HOH A:726BINDING SITE FOR RESIDUE ATP A 400
5AC5SOFTWAREHIS A:27 , SER A:94 , ARG A:228 , ILE A:255 , ASN A:258 , ARG A:264 , SER A:266 , GLY A:317 , GLY A:318 , HOH A:603 , HOH A:604 , HOH A:605 , HOH A:645 , HOH A:724BINDING SITE FOR RESIDUE AMZ A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R7L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:231 -Asn A:232
2Pro A:287 -Pro A:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R7L)

(-) Exons   (0, 0)

(no "Exon" information available for 2R7L)

(-) 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:355
 aligned with PURP_METJA | Q57600 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360 
           PURP_METJA     1 MISKDEILEIFDKYNKDEITIATLGSHTSLHILKGAKLEGFSTVCITMKGRDVPYKRFKVADKFIYVDNFSDIKNEEIQEKLRELNSIVVPHGSFIAYCGLDNVENSFLVPMFGNRRILRWESERSLEGKLLREAGLRVPKKYESPEDIDGTVIVKFPGARGGRGYFIASSTEEFYKKAEDLKKRGILTDEDIANAHIEEYVVGTNFCIHYFYSPLKDEVELLGMDKRYESNIDGLVRIPAKDQLEMNINPSYVITGNIPVVIRESLLPQVFEMGDKLVAKAKELVPPGMIGPFCLQSLCNENLELVVFEMSARVDGGTNSFMNGGPYSFLYNGEPLSMGQRIAREIKMALQLDMIDKIIS 361
               SCOP domains d2r7la1 A:1-123 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                                          d2r7la2 A:124-361 5-formaminoimida      zole-4-carboxamide ribonucleotide synthetase PurP                                                                                                                                                      SCOP domains
               CATH domains 2r7lA01 A:1-111  [code=3.40.50.20, no name defined]                                                            2r7lA02 A:112-139,A:204-361 2r7lA03 A:140-203       ATP-grasp fold, A domain                2r7lA02 A:112-139,A:204-361 ATP-grasp fold, B domain                                                                                                           CATH domains
               Pfam domains --------------------DUF1246-2r7lA02 A:21-144                                                                                                    -----------------------------DUF1297-2r7lA01 A:174-361                                                                                                                                                                    Pfam domains
         Sec.struct. author ..hhhhhhhhhh.......eeeee...hhhhhhhhhhhh...eeeee....hhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhh....ee.hhhhhh...hhhhhhhhhhhhh.....ee.hhhhh...eeee.------...eee.hhhhhhhhhhhhhhh...hhhhhhh.eeee....eeeeeeeeee....eeeeeeeeeeeeeehhhhh..hhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeee...hhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r7l A   1 MISKDEILEIFDKYNKDEITIATLGSHTSLHILKGAKLEGFSTVCITMKGRDVPYKRFKVADKFIYVDNFSDIKNEEIQEKLRELNSIVVPHGSFIAYCGLDNVENSFLVPMFGNRRILRWESERSLEGKLLREAGLRVPKKYESPEDIDGTVIVKF------RGYFIASSTEEFYKKAEDLKKRGILTDEDIANAHIEEYVVGTNFCIHYFYSPLKDEVELLGMDKRYESNIDGLVRIPAKDQLEMNINPSYVITGNIPVVIRESLLPQVFEMGDKLVAKAKELVPPGMIGPFCLQSLCNENLELVVFEMSARVDGGTNSFMNGGPYSFLYNGEPLSMGQRIAREIKMALQLDMIDKIIS 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -   |   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360 
                                                                                                                                                                                      157    164
   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)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: DUF1246] (6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (PURP_METJA | Q57600)
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:0016879    ligase activity, forming carbon-nitrogen bonds    Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, 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.
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:0006188    IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.
    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/Swiss-Prot
        PURP_METJA | Q57600: 2r7k 2r7m 2r7n

(-) Related Entries Specified in the PDB File

2r7k SAME PROTEIN COMPLEXED WITH AMPPCP AND AICAR
2r7m SAME PROTEIN COMPLEXED WITH AMP
2r7n SAME PROTEIN COMPLEXED WITH ADP AND FAICAR