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(-) Description

Title :  CRYSTAL STRUCTURE OF PURP FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ATP
 
Authors :  Y. Zhang, R. H. White, S. E. Ealick
Date :  10 Sep 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Atp-Grasp Superfamily, Unknown Function (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 - PURP PROTEIN PF1517
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: T7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA2Ligand/IonSODIUM ION
4PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA-1Ligand/IonSODIUM ION
4PO46Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA-1Ligand/IonSODIUM ION
4PO46Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:10 , SER A:71 , HIS A:75 , ARG A:238 , SER A:240 , HOH A:642 , HOH A:668BINDING SITE FOR RESIDUE PO4 A 401
02AC2SOFTWAREHIS A:11 , ARG A:202 , ARG A:287 , ALA A:290 , HOH A:612 , HOH A:644 , HOH A:664 , HOH A:665 , HOH A:667BINDING SITE FOR RESIDUE PO4 A 402
03AC3SOFTWAREGLU A:98 , GLU A:104 , ILE A:284 , HOH A:601 , HOH A:673BINDING SITE FOR RESIDUE NA A 600
04AC4SOFTWARESER B:10 , SER B:71 , HIS B:75 , ARG B:238 , SER B:240 , HOH B:603BINDING SITE FOR RESIDUE PO4 B 401
05AC5SOFTWAREHIS B:11 , ARG B:202 , ARG B:287 , ALA B:290 , HOH B:611 , HOH B:618BINDING SITE FOR RESIDUE PO4 B 402
06AC6SOFTWAREGLU B:98 , GLU B:104 , ILE B:284BINDING SITE FOR RESIDUE NA B 600
07AC7SOFTWAREPRO A:116 , LYS A:132 , ALA A:136 , GLY A:138 , TYR A:142 , GLN A:173 , GLU A:174 , TYR A:175 , PHE A:282 , GLU A:283 , HOH A:663 , HOH A:687 , HOH A:691BINDING SITE FOR RESIDUE ATP A 400
08AC8SOFTWAREPRO B:116 , LYS B:132 , TYR B:142 , GLN B:173 , GLU B:174 , ARG B:212 , TYR B:227 , PHE B:282 , HOH B:642BINDING SITE FOR RESIDUE ATP B 400
09AC9SOFTWAREILE A:130 , TYR A:142 , ASP A:217 , TYR A:227BINDING SITE FOR RESIDUE MPD A 500
10BC1SOFTWARETYR A:175 , LEU A:177 , PHE A:221BINDING SITE FOR RESIDUE MPD A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R86)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1His A:134 -Gly A:135
2Ser A:205 -Asn A:206
3Ser B:205 -Asn B:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R86)

(-) Exons   (0, 0)

(no "Exon" information available for 2R86)

(-) 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:334
 aligned with PURP_PYRFU | Q8U0R7 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:334
                                    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    
           PURP_PYRFU     1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKPHGAKGGKGYFLAKDPEDFWRKAEKFLGIKRKEDLKNIQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 334
               SCOP domains d2r86a1 A:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r86a2 A:100-334 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                                                                                                                                                         SCOP domains
               CATH domains 2r86A01 A:1-87  [code=3.40.50.20, no name defined]                                     2r86A02 A:88-115,A:178-334  2r86A03 A:116-177 ATP-grasp fold, A domain                    2r86A02 A:88-115,A:178-334 ATP-grasp fold, B domain                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhh......eee....hhhhhhhh.eee....hhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh......ee.hhhhh...eeeee.........eee.hhhhhhhhhhhhhh..hhhhh..eeeee....eeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee...hhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhh.hhhh.ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r86 A   1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKPHGAKGGKGYFLAKDPEDFWRKAEKFLGIKRKEDLKNIQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 334
                                    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    


Chain B from PDB  Type:PROTEIN  Length:318
 aligned with PURP_PYRFU | Q8U0R7 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:334
                                    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    
           PURP_PYRFU     1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKPHGAKGGKGYFLAKDPEDFWRKAEKFLGIKRKEDLKNIQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 334
               SCOP domains d2r86b1 B:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r86b2 B:100-334 5-formaminoimida      zole-4-carboxamide r          ibonucleotide synthetase PurP                                                                                                                                         SCOP domains
               CATH domains 2r86B01 B:1-87  [code=3.40.50.20, no name defined]                                     2r86B02 B:88-115,B:178-334  2r86B03 B:116-177       ATP-grasp fold, A do          main    2r86B02 B:88-115,B:178-334 ATP-grasp fold, B domain                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhh......eee....hhhhhhhh.eee....hhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee.------...eee.hhhhhhhhhhhh.----------.eeee....eeeeeeeeee....eeeeeeeeeeeeeehhhhh..hhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee...hhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhh.hhhh.ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r86 B   1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKP------KGYFLAKDPEDFWRKAEKFL----------IQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 334
                                    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    
                                                                                                                                                              133    140                159        170
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R86)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PURP_PYRFU | Q8U0R7)
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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  2r86
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  PURP_PYRFU | Q8U0R7
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 Related Entries

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

UniProtKB/Swiss-Prot
        PURP_PYRFU | Q8U0R7: 2r84 2r85 2r87

(-) Related Entries Specified in the PDB File

2r84 SAME PROTEIN WITH COMPLEXED WITH AMP AND AICAR
2r85 SAME PROTEIN WITH COMPLEXED WITH AMP
2r87 SAME PROTEIN WITH COMPLEXED WITH ADP