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(-) Description

Title :  INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: TRP260ALA MUTANT IN COMPLEX WITH 3-DEAZA-ADENOSINE
 
Authors :  W. Versees, S. Loverix, A. Vandemeulebroucke, P. Geerlings, J. Steyaert
Date :  06 Oct 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Aromatic Stacking, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Versees, S. Loverix, A. Vandemeulebroucke, P. Geerlings, J. Steyaert
Leaving Group Activation By Aromatic Stacking: An Alternative To General Acid Catalysis.
J. Mol. Biol. V. 338 1 2004
PubMed-ID: 15050818  |  Reference-DOI: 10.1016/J.JMB.2004.02.049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IAG-NUCLEOSIDE HYDROLASE
    Chains: A, B
    EC Number: 3.2.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: IAG-NH
    Mutation: YES
    Organism Scientific: TRYPANOSOMA VIVAX
    Organism Taxid: 5699

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1AD31Ligand/Ion3-DEAZA-ADENOSINE
2CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , ASP A:15 , THR A:137 , ASP A:261 , HOH A:329 , HOH A:331BINDING SITE FOR RESIDUE CA A 328
2AC2SOFTWAREASP B:10 , ASP B:15 , THR B:137 , ASP B:261 , AD3 B:330 , HOH B:331BINDING SITE FOR RESIDUE CA B 329
3AC3SOFTWAREASN B:12 , ASP B:14 , ASP B:15 , ASP B:40 , TRP B:83 , THR B:137 , MET B:164 , ASN B:173 , GLU B:184 , ASN B:186 , ASP B:261 , CA B:329 , HOH B:331BINDING SITE FOR RESIDUE AD3 B 330

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R4F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R4F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R4F)

(-) Exons   (0, 0)

(no "Exon" information available for 1R4F)

(-) 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:314
 aligned with Q9GPQ4_TRYVI | Q9GPQ4 from UniProtKB/TrEMBL  Length:327

    Alignment length:327
                                    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       
         Q9GPQ4_TRYVI     1 MAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTHCELLRDGDGYYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAEKYPLTFVARNPEAEFFLDMLLRSARAC 327
               SCOP domains d1r4fa_ A: Inosine-adenosine-guanosine preferring nucleoside hydrolase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1r4fA00 A:0-327 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhhhh........eee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.eeeeeee...................hhhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhheeeeeeeee..........eee.......eeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r4f A   0 SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAM-------------YAADALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC 327
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   |     -       260       270       280       290       300       310       320       
                            ||                                                                                                                                                                                                                                               244           258                                                                     
                            0|                                                                                                                                                                                                                                                                                                                                     
                             2                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with Q9GPQ4_TRYVI | Q9GPQ4 from UniProtKB/TrEMBL  Length:327

    Alignment length:327
                                    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       
         Q9GPQ4_TRYVI     1 MAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTHCELLRDGDGYYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAEKYPLTFVARNPEAEFFLDMLLRSARAC 327
               SCOP domains d1r4fb_ B: Inosine-adenosine-guanosine preferring nucleoside hydrolase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1r4fB00 B:0-327 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -IU_nuc_hydro-1r4fB01 B:2-327                                                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) -IU_nuc_hydro-1r4fB02 B:2-327                                                                                                                                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.eeeeeee...................hhhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhheeeee.eee..........eee........eeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r4f B   0 SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAM-------------YAADALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC 327
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   |     -       260       270       280       290       300       310       320       
                            0|                                                                                                                                                                                                                                               244           258                                                                     
                             2
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: IU_nuc_hydro] (7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9GPQ4_TRYVI | Q9GPQ4)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  1r4f
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 Related Entries

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

UniProtKB/TrEMBL
        Q9GPQ4_TRYVI | Q9GPQ4: 1hoz 1hp0 1kic 1kie 2ff1 2ff2 3b9g 3epw 3epx

(-) Related Entries Specified in the PDB File

1hoz CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE- PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX
1hp0 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE- PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX IN COMPLEX WITH THE SUBSTRATE ANALOGUE 3-DEAZA-ADENOSINE
1kic INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN COMPLEX WITH INOSINE
1kie INOSINE-ADENOSINE-GUANOSINE PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN COMPLEX WITH 3- DEAZA-ADENOSINE
1mas PURINE NUCLEOSIDE HYDROLASE FROM CRITHIDIA FASCICULATA
2mas PURINE NUCLEOSIDE HYDROLASE FROM CRITHIDIA FASCICULATA WITH A TRANSITION STATE INHIBITOR