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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MANGANESE IONS.
 
Authors :  J. Martinez, V. Truffault, M. Hothorn
Date :  23 Jun 15  (Deposition) - 05 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Tripolyphosphate, Triphosphate Tunnel Metalloenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Martinez, V. Truffault, M. Hothorn
Structural Determinants For Substrate Binding And Catalysis In Triphosphate Tunnel Metalloenzymes.
J. Biol. Chem. V. 290 23348 2015
PubMed-ID: 26221030  |  Reference-DOI: 10.1074/JBC.M115.674473

(-) Compounds

Molecule 1 - INORGANIC TRIPHOSPHATASE
    Chains: A
    EC Number: 3.6.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
13PO1Ligand/IonTRIPHOSPHATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:252 , ARG A:402 , HIS A:403 , ALA A:406 , HOH A:2224BINDING SITE FOR RESIDUE EDO A1000
2AC2SOFTWAREGLU A:17 , ARG A:348 , HIS A:349 , ARG A:371 , ARG A:374 , HOH A:2240BINDING SITE FOR RESIDUE EDO A1001
3AC3SOFTWAREARG A:20 , TYR A:125 , GLU A:127 , LEU A:142 , GLN A:144 , ALA A:351 , HOH A:2019BINDING SITE FOR RESIDUE EDO A1002
4AC4SOFTWAREGLU A:6 , GLU A:160 , 3PO A:500 , MN A:502BINDING SITE FOR RESIDUE MN A 501
5AC5SOFTWAREGLU A:4 , GLU A:6 , GLU A:162 , 3PO A:500 , MN A:501 , HOH A:2003 , HOH A:2008BINDING SITE FOR RESIDUE MN A 502
6AC6SOFTWAREGLU A:4 , GLU A:6 , LYS A:8 , ARG A:56 , ARG A:58 , LYS A:69 , ARG A:81 , PHE A:124 , ARG A:126 , GLU A:160 , SER A:190 , LYS A:191 , MN A:501 , MN A:502 , HOH A:2004 , HOH A:2031 , HOH A:2032BINDING SITE FOR RESIDUE 3PO A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A61)

(-) Exons   (0, 0)

(no "Exon" information available for 5A61)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...hhhhhhhhhh.....................hhhhhh.....................eee..eeeeeeeeeee.....hhhhhhhhhh.......hhhhhh..................................................hhhhhhhhhhhhh....eee...hhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a61 A   0 AMAQEIELKFIVNHSAVEALRDHLNTLGGEHHDPVQLLNIYYETPDNWLRGHDMGLRIRGENGRYEMTMKVAGRVTGGLHQRPEYNVALSEPTLDLAQLPTEVWPNGELPADLASRVQPLFSTDFYREKWLVAVDDSRIEIALDQGEVKAGEFAEPICELELELLSGDTRAVLKLANQLVSQTGLRQGSLSKAARGYHLAQGNPAREIKPTTILHVAAKADVEQGLEAAFELALAQWQYHEELWVRGNDAAKEQVLAAIGLVRHALMLFGGIVPRKASTHLRDLLTQCEATIASAVSAVTAVYSTETAMAKLALTEWLVSKAWQPFLDAKAQGKISDSFKRFADIHLSRHAAELKSVFCQPLGDRYHDQLPRLTRDIDSILLLAGYYDPVVAQAWLENWQGLRHAIATGQRIEIEHFRNEANNQEPFWL 428
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
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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  (0, 0)

(no "SCOP Domain" information available for 5A61)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A61)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a61
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 Related Entries

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

UniProtKB/Swiss-Prot
        3PASE_ECOLI | P30871: 5a60
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(-) Related Entries Specified in the PDB File

5a5y CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MAGNESIUM ION (FORM A)
5a60 CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MAGNESIUM IONS
5a64 CRYSTAL STRUCTURE OF MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE TRIPHOSPHATE.
5a65 CRYSTAL STRUCTURE OF MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE DIPHOSPHATE, ORTHOPHOSPHATE AND MAGNESIUM IONS.
5a66 CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM A)
5a67 CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM B)
5a68 CRYSTAL STRUCTURE OF THE ATTTM3 PRODUCT COMPLEX WITH TWO ORTHOPHOSPHATES AND MANGANESE IONS (FORM B)