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(-) Description

Title :  CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM A)
 
Authors :  J. Martinez, V. Truffault, M. Hothorn
Date :  24 Jun 15  (Deposition) - 05 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Inorganic Polyphosphate, 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 - TRIPHOSPHATE TUNEL METALLOENZYME 3
    Chains: A, B
    EC Number: 3.6.1.3, 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 Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: COL0
    Synonym: ADENOSINETRIPHOSPHATASE, ATPASE, TRIPHOSPHATASE, PPPASE, INORGANIC TRIPHOSPHATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
13PO2Ligand/IonTRIPHOSPHATE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
13PO1Ligand/IonTRIPHOSPHATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13PO1Ligand/IonTRIPHOSPHATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:4 , LYS A:6 , ARG A:52 , ARG A:54 , LYS A:76 , ARG A:143 , GLU A:169 , THR A:199 , LYS A:200 , MN A:1001 , HOH A:2003 , HOH A:2004 , HOH A:2020 , HOH A:2032 , HOH A:2043 , HOH A:2103BINDING SITE FOR RESIDUE 3PO A1000
02AC2SOFTWAREGLU A:4 , GLU A:169 , 3PO A:1000BINDING SITE FOR RESIDUE MN A1001
03AC3SOFTWAREARG A:8 , LEU A:9 , ASN A:164 , CYS A:165 , TYR A:166BINDING SITE FOR RESIDUE EDO A1101
04AC4SOFTWAREPHE A:37 , ASP A:38 , SER A:45 , ALA A:49 , VAL A:50 , LEU A:51 , PHE A:201BINDING SITE FOR RESIDUE EDO A1102
05AC5SOFTWAREALA A:13 , ALA A:14 , ARG A:17 , SER A:106 , LYS A:190 , GLU A:192 , HOH A:2063BINDING SITE FOR RESIDUE EDO A1103
06AC6SOFTWAREGLU A:174 , PRO A:175 , GLU A:176 , ARG A:177BINDING SITE FOR RESIDUE EDO A1104
07AC7SOFTWAREGLU B:4 , LYS B:6 , ARG B:52 , ARG B:54 , LYS B:76 , ARG B:143 , GLU B:169 , THR B:199 , LYS B:200 , MN B:1001 , HOH B:2003 , HOH B:2026 , HOH B:2041 , HOH B:2115 , HOH B:2118BINDING SITE FOR RESIDUE 3PO B1000
08AC8SOFTWAREGLU B:4 , GLU B:169 , 3PO B:1000BINDING SITE FOR RESIDUE MN B1001
09AC9SOFTWAREGLU B:174 , PRO B:175 , GLU B:176 , ARG B:177BINDING SITE FOR RESIDUE EDO B1100
10BC1SOFTWAREPRO A:24 , HIS A:26 , TYR B:25 , ARG B:149 , HOH B:2120BINDING SITE FOR RESIDUE EDO B1101
11BC2SOFTWAREARG A:149 , MET A:181 , HOH A:2083 , ARG B:177BINDING SITE FOR RESIDUE EDO B1102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A66)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A66)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A66)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A66)

(-) Exons   (0, 0)

(no "Exon" information available for 5A66)

(-) 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    
   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:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhh..eeeeeeeeeeeee...hhhhhh..eeeeeeeee...........eeeeeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeeeeeeeeeeee..eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a66 A   0 AMEVEVKLRLLTAAAHLRLTTLLTPYHLKTLHQRNTFFDTPKNDLSLRRAVLRLRFLQNAAVSAASPSPPRCIVSLKAKPTLANGISRVEEDEEEIEYWIGKECVESPAKLSDIGSRVLKRVKEEYGFNDFLGFVCLGGFENVRNVYEWRGVKLEVDETKYDFGNCYEIECETEEPERVKTMIEEFLTEEKIEFSNSDMTKFAVFRSGKLP 210
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhh..eeeeeeeeeeeee...hhhhhh.eeeeeeeeee...........eeeeeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeeeeeeeeeeee..eeeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a66 B   0 AMEVEVKLRLLTAAAHLRLTTLLTPYHLKTLHQRNTFFDTPKNDLSLRRAVLRLRFLQNAAVSAASPSPPRCIVSLKAKPTLANGISRVEEDEEEIEYWIGKECVESPAKLSDIGSRVLKRVKEEYGFNDFLGFVCLGGFENVRNVYEWRGVKLEVDETKYDFGNCYEIECETEEPERVKTMIEEFLTEEKIEFSNSDMTKFAVFRSGKLP 210
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   Legend:   → Mismatch (orange background)
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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 5A66)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A66)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A66)

(-) Gene Ontology  (7, 7)

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  5a66
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  3.6.1.25
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 Related Entries

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

UniProtKB/Swiss-Prot
        TTM3_ARATH | Q9SIY3: 3v85 5a5y 5a67 5a68

(-) 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
5a61 CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MANGANESE 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.
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)