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(-) Description

Title :  CRYSTAL STRUCTURE OF PURP FROM PYROCOCCUS FURIOSUS COMPLEXED WITH AMP AND AICAR
 
Authors :  Y. Zhang, R. H. White, S. E. Ealick
Date :  10 Sep 07  (Deposition) - 04 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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 Synthetas From Methanocaldococcus Jannaschii.
Biochemistry V. 47 205 2008
PubMed-ID: 18069798  |  Reference-DOI: 10.1021/BI701406G

(-) 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  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2AMZ2Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
3CL2Ligand/IonCHLORIDE ION
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA2Ligand/IonSODIUM ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1AMP3Ligand/IonADENOSINE MONOPHOSPHATE
2AMZ3Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
3CL-1Ligand/IonCHLORIDE ION
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1AMP3Ligand/IonADENOSINE MONOPHOSPHATE
2AMZ3Ligand/IonAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
3CL-1Ligand/IonCHLORIDE ION
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:98 , GLU A:104 , ILE A:284 , HOH A:602 , HOH A:621BINDING SITE FOR RESIDUE NA A 600
02AC2SOFTWAREHIS A:11 , ARG A:202 , ARG A:287 , ALA A:290 , HOH A:894BINDING SITE FOR RESIDUE CL A 601
03AC3SOFTWAREGLU B:98 , GLU B:104 , ILE B:284 , HOH B:795 , HOH B:796 , HOH B:842BINDING SITE FOR RESIDUE NA B 600
04AC4SOFTWAREHIS B:11 , ARG B:287 , ALA B:290 , HOH B:837BINDING SITE FOR RESIDUE CL B 601
05AC5SOFTWAREILE A:130 , LYS A:132 , TYR A:142 , GLN A:173 , GLU A:174 , TYR A:175 , ARG A:212 , HOH A:610 , HOH A:612 , HOH A:615 , HOH A:616 , HOH A:823 , HOH A:931BINDING SITE FOR RESIDUE AMP A 400
06AC6SOFTWARESER A:10 , HIS A:11 , GLY A:70 , SER A:71 , HIS A:75 , ARG A:202 , ASN A:232 , ARG A:238 , SER A:240 , ALA A:290 , HOH A:603 , HOH A:606 , HOH A:607 , HOH A:608 , HOH A:609 , HOH A:781BINDING SITE FOR RESIDUE AMZ A 401
07AC7SOFTWAREPRO B:116 , ILE B:130 , LYS B:132 , TYR B:142 , GLN B:173 , GLU B:174 , TYR B:175 , GLU B:283 , HOH B:698 , HOH B:700 , HOH B:701 , HOH B:702 , HOH B:767BINDING SITE FOR RESIDUE AMP B 400
08AC8SOFTWARESER B:10 , HIS B:11 , GLY B:70 , SER B:71 , HIS B:75 , ARG B:202 , ASN B:232 , ARG B:238 , SER B:240 , ALA B:290 , HOH B:603 , HOH B:606 , HOH B:607 , HOH B:608 , HOH B:609 , HOH B:829BINDING SITE FOR RESIDUE AMZ B 401
09AC9SOFTWARETYR A:142 , ASP A:217 , TYR A:227 , HOH A:779BINDING SITE FOR RESIDUE MPD A 500
10BC1SOFTWARETYR A:175 , LEU A:177 , ILE A:213 , PHE A:221 , HOH A:834 , HOH A:835BINDING SITE FOR RESIDUE MPD A 501
11BC2SOFTWARETYR B:175 , LEU B:177 , ILE B:213 , PHE B:221 , MET B:223 , HOH B:856BINDING SITE FOR RESIDUE MPD B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R84)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:205 -Asn A:206
2Ser B:205 -Asn B:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R84)

(-) Exons   (0, 0)

(no "Exon" information available for 2R84)

(-) 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:329
 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 d2r84a1 A:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r84a2 A:100-334 5-formaminoimida     zole-4-carboxamide ribonucleotide synthetase PurP                                                                                                                                                    SCOP domains
               CATH domains 2r84A01 A:1-87  [code=3.40.50.20, no name defined]                                     2r84A02 A:88-115,A:178-334  2r84A03 A:116-177      ATP-grasp fold, A domain               2r84A02 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...hhhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee.-----....eee.hhhhhhhhhhhhhh..hhhhh...eeee....eeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee...hhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhh.hhhh.ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r84 A   1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKP-----GKGYFLAKDPEDFWRKAEKFLGIKRKEDLKNIQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 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    
                                                                                                                                                              133   139                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:313
 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 d2r84b1 B:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r84b2 B:100-334 5-formaminoimid        azole-4-carboxam             ide ribonucleotide synthetase PurP                                                                                                                                    SCOP domains
               CATH domains 2r84B01 B:1-87  [code=3.40.50.20, no name defined]                                     2r84B02 B:88-115,B:178-334  2r84B03 B:116-177         ATP-grasp fold,              A domai2r84B02 B:88-115,B:178-334 ATP-grasp fold, B domain                                                                                                           CATH domains
           Pfam domains (1) ----DUF1246-2r84B03 B:5-120                                                                                             ------------        ---------DUF1297             -2r84B01 B:150-334                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ----DUF1246-2r84B04 B:5-120                                                                                             ------------        ---------DUF1297             -2r84B02 B:150-334                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...eeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhh......eee....hhhhhhhh.eee...hhhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee--------..eee.hhhhhhhhhh-------------.eeee....eeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee...hhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhh.hhhh.ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r84 B   1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVK--------GYFLAKDPEDFWRKAE-------------IQIQEYVLGVPVYPHYFYSKVREELELMSIDRRYESNVDAIGRIPAKDQLEFDMDITYTVIGNIPIVLRESLLMDVIEAGERVVKAAEELMGGLWGPFCLEGVFTPDLEFVVFEISARIVAGTNIFVNGSPYTWLRYDRPVSTGRRIAMEIREAIENDMLEKVLT 334
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |       -|      150     |   -       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330    
                                                                                                                                                             132      141            156           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  (2, 4)

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,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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  2r84
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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: 2r85 2r86 2r87

(-) Related Entries Specified in the PDB File

2r85 SAME PROTEIN WITH COMPLEXED WITH AMP
2r86 SAME PROTEIN WITH COMPLEXED WITH ATP
2r87 SAME PROTEIN WITH COMPLEXED WITH ADP