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(-) Description

Title :  'X-RAY CRYSTAL STRUCTURE OF THE PUTATIVE N-TYPE ATP PYROPHOSPHATASE (PF0828) IN COMPLEX WITH ATP FROM PYROCOCCUS FURIOSUS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET PFR23
 
Authors :  F. Forouhar, J. Seetharaman, J. Janjua, R. Xiao, K. Cunningham, L. Ma, R J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt Northeast Structural Genomics Consortium (Nesg)
Date :  16 Apr 11  (Deposition) - 11 May 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, Alpha-Beta Protein That Binds Atp And Amp, N-Type Atp Pyrophosphatase, Atp And Amp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, N. Saadat, M. Hussain, J. Seetharaman, I. Lee, H. Janjua, R. Xiao, R. Shastry, T. B. Acton, G. T. Montelione, L. Tong
A Large Conformational Change In The Putative Atp Pyrophosphatase Pf0828 Induced By Atp Binding.
Acta Crystallogr. , Sect. F V. 67 1323 2011
PubMed-ID: 22102225  |  Reference-DOI: 10.1107/S1744309111031447

(-) Compounds

Molecule 1 - N-TYPE ATP PYROPHOSPHATASE SUPERFAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PF0828
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:10 , SER A:12 , GLY A:14 , LYS A:15 , ASP A:16 , SER A:17 , VAL A:35 , MSE A:37 , TYR A:47 , HIS A:48 , ALA A:96 , GLY A:97 , GLN A:104 , GLU A:188 , THR A:189 , HOH A:288BINDING SITE FOR RESIDUE ATP A 301
2AC2SOFTWAREALA A:128 , HIS A:179 , VAL A:180 , ALA A:181 , GLU A:183 , HOH A:318BINDING SITE FOR RESIDUE PO4 A 302
3AC3SOFTWARELYS A:77 , GLU A:80 , ASP A:81 , ARG A:84 , LYS A:208 , VAL A:209 , TRP A:210 , HOH A:291BINDING SITE FOR RESIDUE PO4 A 303
4AC4SOFTWARELEU B:10 , SER B:12 , GLY B:14 , LYS B:15 , ASP B:16 , SER B:17 , VAL B:35 , MSE B:37 , TYR B:47 , HIS B:48 , ALA B:96 , GLY B:97 , GLN B:104 , HOH B:238 , HOH B:246 , HOH B:283BINDING SITE FOR RESIDUE ATP B 301
5AC5SOFTWAREGLU B:42 , HIS B:48 , THR B:49 , ILE B:50 , GLU B:188 , LYS B:218BINDING SITE FOR RESIDUE PO4 B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RK1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RK1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RK1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RK1)

(-) Exons   (0, 0)

(no "Exon" information available for 3RK1)

(-) 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:221
 aligned with Q8U2K6_PYRFU | Q8U2K6 from UniProtKB/TrEMBL  Length:229

    Alignment length:225
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
         Q8U2K6_PYRFU     5 ADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYHTINANLTDLQARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGALASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESK 229
               SCOP domains d3rk1a_ A: Putative N-type ATP pyrophosphatase PF0828                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhh..eee..----hhhhhhhhhhhh..eeeeeee.....hhhhh....hhhhhhhhhhhhhhh..........eeeeeee......eeeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rk1 A   5 ADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTmVSENEESYmYHTINANLTDLQARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGALASKYQRKRIEKVAKELGLEVYTP----DAKEYmRELLNLGFKImVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDmPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESK 229
                                    14        24        34  |     44 |      54        64        74        84        94       104       114       | -  |    134       144       154       164       174       184       194       204       214       224     
                                                           37-MSE   46-MSE                                                                     122  127    |        143-MSE                                            194-MSE                               
                                                                                                                                                         132-MSE                                                                                             


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with Q8U2K6_PYRFU | Q8U2K6 from UniProtKB/TrEMBL  Length:229

    Alignment length:227
                                                                                                                                                                                                                                                           229 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     | 
         Q8U2K6_PYRFU     4 LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYHTINANLTDLQARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGALASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESK-   -
               SCOP domains d3rk1b_ B: Putative N-type ATP pyrophosphatase PF0828                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -ATP_bind_4-3rk1B01 B:5-226                                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -ATP_bind_4-3rk1B02 B:5-226                                                                                                                                                                                                    ---- Pfam domains (2)
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeeeeeee..............hhhhhhhhhh..eeeeee....hhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh.eee..----hhhhhhhhhhhh..eeeeeee.....hhhhh....hhhhhhhhhhhhhhhh.........eeeeeee......eeeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rk1 B   4 LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTmVSENEESYmYHTINANLTDLQARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGALASKYQRKRIEKVAKELGLEVYTP----DAKEYmRELLNLGFKImVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDmPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKL 230
                                    13        23        33   |    43  |     53        63        73        83        93       103       113        |-   |   133       143       153       163       173       183       193|      203       213       223       
                                                            37-MSE   46-MSE                                                                     122  127    |        143-MSE                                            194-MSE                                
                                                                                                                                                          132-MSE
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  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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RK1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8U2K6_PYRFU | Q8U2K6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8U2K6_PYRFU | Q8U2K6: 3rjz 3rk0

(-) Related Entries Specified in the PDB File

3rjz THIS IS THE APO STRUCTURE
3rk0 THIS IS THE AMP-BOUND STRUCTURE RELATED ID: PFR23 RELATED DB: TARGETDB