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(-) Description

Title :  STRUCTURE OF THE E. COLI INOSINE TRIPHOSPHATE PYROPHOSPHATASE RGDB IN COMPLEX WITH ITP
 
Authors :  A. U. Singer, R. Lam, M. Proudfoot, T. Skarina, A. Savchenko, A. F. Yakun
Date :  23 May 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Itp Pyrophosphatase X-Ray Structure Enzyme Mechanism Substrate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Savchenko, M. Proudfoot, T. Skarina, A. Singer, O. Litvinova, R. Sanishvili, G. Brown, N. Chirgadze, A. F. Yakunin
Molecular Basis Of The Antimutagenic Activity Of The House-Cleaning Inosine Triphosphate Pyrophosphatase Rdgb From Escherichia Coli.
J. Mol. Biol. V. 374 1091 2007
PubMed-ID: 17976651  |  Reference-DOI: 10.1016/J.JMB.2007.10.012

(-) Compounds

Molecule 1 - HAM1 PROTEIN HOMOLOG
    Chains: A, B
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15-B-BASED P11
    Expression System Strain: BL21(DE3) CODON PLUS RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YGGV
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ITT2Ligand/IonINOSINE 5'-TRIPHOSPHATE
3MSE3Mod. Amino AcidSELENOMETHIONINE
4NA5Ligand/IonSODIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:41 , ITT A:6246 , HOH A:6450 , HOH A:6455BINDING SITE FOR RESIDUE CA A 200
02AC2SOFTWAREASN A:10 , ASP A:95 , PHE A:154 , ITT A:6246 , HOH A:6268BINDING SITE FOR RESIDUE NA A 201
03AC3SOFTWAREILE A:83 , SER A:85 , ALA A:86 , ITT A:6246 , HOH A:6372BINDING SITE FOR RESIDUE NA A 202
04AC4SOFTWAREGLU A:16 , SER A:181BINDING SITE FOR RESIDUE NA A 203
05AC5SOFTWAREARG A:195 , ASP B:75 , ARG B:117BINDING SITE FOR RESIDUE SO4 A 6245
06AC6SOFTWAREGLU B:41 , ITT B:203 , HOH B:347BINDING SITE FOR RESIDUE CA B 200
07AC7SOFTWAREASN B:10 , ASP B:95 , ITT B:203 , HOH B:237BINDING SITE FOR RESIDUE NA B 201
08AC8SOFTWAREASP B:95 , ASN B:98 , TYR B:156 , ITT B:203 , HOH B:227BINDING SITE FOR RESIDUE NA B 202
09AC9SOFTWARETHR A:8 , GLY A:9 , ASN A:10 , LYS A:13 , GLU A:41 , LYS A:53 , ASP A:68 , ALA A:69 , SER A:70 , GLY A:71 , SER A:85 , ALA A:86 , PHE A:118 , PHE A:154 , GLY A:155 , TYR A:156 , ASP A:157 , LYS A:177 , HIS A:182 , ARG A:183 , CA A:200 , NA A:201 , NA A:202 , HOH A:6251 , HOH A:6268 , HOH A:6274 , HOH A:6323 , HOH A:6328 , HOH A:6450 , HOH A:6455BINDING SITE FOR RESIDUE ITT A 6246
10BC1SOFTWARETHR B:8 , GLY B:9 , ASN B:10 , LYS B:13 , GLU B:41 , LYS B:53 , ASP B:68 , ALA B:69 , SER B:70 , GLY B:71 , SER B:85 , ALA B:86 , PHE B:118 , PHE B:154 , GLY B:155 , TYR B:156 , ASP B:157 , LYS B:177 , HIS B:182 , ARG B:183 , CA B:200 , NA B:201 , NA B:202 , HOH B:232 , HOH B:237 , HOH B:264 , HOH B:360 , HOH B:364BINDING SITE FOR RESIDUE ITT B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q16)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:80 -Pro A:81
2Ala B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q16)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q16)

(-) 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:197
 aligned with IXTPA_ECOLI | P52061 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          IXTPA_ECOLI     1 MQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADDSGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRNG 197
               SCOP domains d2q16a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains -2q16A00 A:2-197  [code=3.90.950.10, no name defined]                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhh.eeee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhh...hhhh.eeeeeeeeeee........eeeeeeeeeee...........hhh.ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q16 A   1 mQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADASGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETmKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRNG 197
                            |       10        20        30        40        50        60        70        80        90       100     | 110       120       130       140       150       160       170       180       190       
                            |                                                                                                      106-MSE                                                                                       
                            1-MSE                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with IXTPA_ECOLI | P52061 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
          IXTPA_ECOLI     3 KVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADDSGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALR 195
               SCOP domains d2q16b_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2q16B00 B:3-195  [code=3.90.950.10, no name defined]                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhh..eee.hhhh.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh........hhhhhhhhhhhhh...hhhh.eeeeeeeeeee........eeeeeeeeeee...........hhh.ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q16 B   3 KVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADASGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETmKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALR 195
                                    12        22        32        42        52        62        72        82        92       102   |   112       122       132       142       152       162       172       182       192   
                                                                                                                                 106-MSE
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q16)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IXTPA_ECOLI | P52061)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
    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:0009143    nucleoside triphosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving 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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IXTPA_ECOLI | P52061: 1k7k 2pyu

(-) Related Entries Specified in the PDB File

1k7k STRUCTURE OF APO-RGDB
2pyu RGDB IN COMPLEX WITH IMP