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(-) Description

Title :  CRYSTAL STRUCTURE OF NDX2 IN COMPLEX WITH MG2+ FROM THERMUS THERMOPHILUS HB8
 
Authors :  T. Wakamatsu, N. Nakagawa, S. Kuramitsu, S. Yokoyama, R. Masui, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Apr 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudix Protein, Adp-Ribose, Fad, Thermus Thermophilus, Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wakamatsu, N. Nakagawa, S. Kuramitsu, R. Masui
Structural Basis For Different Substrate Specificities Of Two Adp-Ribose Pyrophosphatases From Thermus Thermophilus Hb8
J. Bacteriol. V. 190 1108 2008
PubMed-ID: 18039767  |  Reference-DOI: 10.1128/JB.01522-07

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NDX2
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: NDX2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:90 , GLU A:94 , GLU A:139 , HOH A:1007 , HOH A:1015 , HOH A:1036BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREALA A:74 , GLU A:94 , GLU A:139 , HOH A:1004 , HOH A:1013 , HOH A:1015 , HOH A:1037BINDING SITE FOR RESIDUE MG A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Gly A:39 -Pro A:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVM)

(-) 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    
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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:182
 aligned with Q5SJY9_THET8 | Q5SJY9 from UniProtKB/TrEMBL  Length:182

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
         Q5SJY9_THET8     1 MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEGETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEIQDASTALTLFYAEPHLKRLGLL 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------NUDIX-2yvmA01 A:40-171                                                                                                              ----------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....eeeeeee.....eeeeee.....eeeeeee.....eeeeeeee.hhhh.eeee..eee.....hhhhhhhhhhhhhhhee...eee.............eeeeeee...ee...........eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvm A   1 MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEGETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEIQDASTALTLFYAEPHLKRLGLL 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2YVM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YVM)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SJY9_THET8 | Q5SJY9)
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.
    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

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UniProtKB/TrEMBL
        Q5SJY9_THET8 | Q5SJY9: 2yvn 2yvo 2yvp

(-) Related Entries Specified in the PDB File

2yvn
2yvo
2yvp RELATED ID: TTK003001256.1 RELATED DB: TARGETDB