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(-) Description

Title :  CRYSTAL STRUCTURE OF PURP FROM PYROCOCCUS FURIOSUS COMPLEXED WITH AMP
 
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 :  1.70
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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1AMP6Ligand/IonADENOSINE MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1AMP6Ligand/IonADENOSINE MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:98 , GLU A:104 , ILE A:284 , HOH A:613 , HOH A:746 , HOH A:747BINDING SITE FOR RESIDUE NA A 600
02AC2SOFTWAREHIS A:11 , ALA A:290 , HOH A:756 , HOH A:759BINDING SITE FOR RESIDUE CL A 601
03AC3SOFTWAREGLU B:98 , GLU B:104 , ILE B:284 , HOH B:679 , HOH B:680 , HOH B:681BINDING SITE FOR RESIDUE NA B 600
04AC4SOFTWAREHIS B:11 , ALA B:290 , HOH B:690 , HOH B:695BINDING SITE FOR RESIDUE CL B 601
05AC5SOFTWAREPRO A:116 , ILE A:130 , LYS A:132 , TYR A:142 , GLN A:173 , GLU A:174 , TYR A:175 , ARG A:212 , TYR A:227 , HOH A:608 , HOH A:765 , HOH A:766 , HOH A:793 , HOH A:794 , HOH A:875 , HOH A:876 , HOH A:878 , HOH A:879BINDING SITE FOR RESIDUE AMP A 400
06AC6SOFTWARESER A:10 , SER A:71 , ALA A:74 , HIS A:75 , ARG A:238 , SER A:240 , LEU A:277 , HOH A:607 , HOH A:751 , HOH A:777BINDING SITE FOR RESIDUE AMP A 401
07AC7SOFTWAREPRO B:116 , ILE B:130 , LYS B:132 , TYR B:142 , GLN B:173 , GLU B:174 , TYR B:175 , ARG B:212 , HOH B:666 , HOH B:675 , HOH B:734 , HOH B:735 , HOH B:858BINDING SITE FOR RESIDUE AMP B 400
08AC8SOFTWARESER B:10 , SER B:71 , ALA B:74 , HIS B:75 , ARG B:238 , SER B:240 , LEU B:277 , HOH B:606 , HOH B:692 , HOH B:693BINDING SITE FOR RESIDUE AMP B 401
09AC9SOFTWARETYR A:142 , PHE A:143 , ASP A:217 , TYR A:227 , HOH A:666 , HOH A:730BINDING SITE FOR RESIDUE MPD A 500
10BC1SOFTWARETYR A:175 , LEU A:177 , ILE A:213 , PHE A:221 , HOH A:960BINDING SITE FOR RESIDUE MPD A 501
11BC2SOFTWARETYR B:142 , TYR B:175 , PRO B:214 , ASP B:217 , TYR B:227 , HOH B:720BINDING SITE FOR RESIDUE MPD B 500
12BC3SOFTWARETYR B:175 , LEU B:177 , ILE B:213 , PHE B:221 , HOH B:859 , HOH B:860BINDING SITE FOR RESIDUE MPD B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R85)

(-) 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 2R85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R85)

(-) Exons   (0, 0)

(no "Exon" information available for 2R85)

(-) 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:330
 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 d2r85a1 A:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r85a2 A:100-334 5-formaminoimidaz    ole-4-carboxamide ribonucleotide synthetase PurP                                                                                                                                                     SCOP domains
               CATH domains 2r85A01 A:1-87  [code=3.40.50.20, no name defined]                                     2r85A02 A:88-115,A:178-334  2r85A03 A:116-177 A    TP-grasp fold, A domain                2r85A02 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.........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
                 2r85 A   1 MKVRIATYASHSALQILKGAKDEGFETIAFGSSKVKPLYTKYFPVADYFIEEKYPEEELLNLNAVVVPTGSFVAHLGIELVENMKVPYFGNKRVLRWESDRNLERKWLKKAGIRVPEVYEDPDDIEKPVIVKPH----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    
                                                                                                                                                               134  139                                                                                                                                                                                                   


Chain B 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 d2r85b1 B:1-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                   d2r85b2 B:100-334 5-formaminoimida     zole-4-carboxamide ribonucleotide synthetase PurP                                                                                                                                                    SCOP domains
               CATH domains 2r85B01 B:1-87  [code=3.40.50.20, no name defined]                                     2r85B02 B:88-115,B:178-334  2r85B03 B:116-177      ATP-grasp fold, A domain               2r85B02 B:88-115,B:178-334 ATP-grasp fold, B domain                                                                                                           CATH domains
           Pfam domains (1) ----DUF1246-2r85B03 B:5-120                                                                                             -----------------------------DUF1297-2r85B01 B:150-334                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ----DUF1246-2r85B04 B:5-120                                                                                             -----------------------------DUF1297-2r85B02 B:150-334                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ...eeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhh......eee....hhhhhhhh.eee....hhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh.........hhhhh...eeee.-----....eee.hhhhhhhhhhhhh...........eeee....eeeeeeeeee....eeeeeeeeeeeeee.hhhhhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee...hhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhh.hhhhhee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r85 B   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
   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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  2r85
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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 2r86 2r87

(-) Related Entries Specified in the PDB File

2r84 SAME PROTEIN WITH COMPLEXED WITH AMP AND AICAR
2r86 SAME PROTEIN WITH COMPLEXED WITH ATP
2r87 SAME PROTEIN WITH COMPLEXED WITH ADP