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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE INORGANIC TRIPHOSPHATASE NE1496
 
Authors :  V. V. Lunin, T. Skarina, O. Onopriyenko, T. A. Binkowski, A. Joachimiak A. M. Edwards, A. Savchenko
Date :  26 Sep 11  (Deposition) - 09 May 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inorganic Triphosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Delvaux, M. R. V. S. Murty, V. Gabelica, B. Lakaye, V. V. Lunin, T. Skarina, O. Onopriyenko, G. Kohn, P. Wins, E. De Pauw, L. Bettendorff
A Specific Inorganic Triphosphatase From Nitrosomonas Europaea: Structure And Catalytic Mechanism.
J. Biol. Chem. V. 286 34023 2011
PubMed-ID: 21840996

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NE1496
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 915

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NA8Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:130 , PHE A:132 , HOH A:173 , HOH A:186 , HOH A:240 , HOH A:246BINDING SITE FOR RESIDUE NA A 154
02AC2SOFTWAREGLY A:80 , ALA A:148 , SER A:150 , HOH A:177 , HOH A:182BINDING SITE FOR RESIDUE NA A 155
03AC3SOFTWAREHIS A:106 , SER A:108 , HOH A:193 , HOH A:261 , HOH A:265BINDING SITE FOR RESIDUE NA A 156
04AC4SOFTWAREPRO A:32 , ASP A:34 , ASP A:94 , HOH A:187 , HOH A:254 , HOH A:354BINDING SITE FOR RESIDUE NA A 157
05AC5SOFTWAREARG A:82 , VAL A:83 , GLU A:84 , ALA A:104 , LEU A:107 , HOH A:180BINDING SITE FOR RESIDUE EDO A 158
06AC6SOFTWAREPRO B:130 , PHE B:132 , HOH B:174 , HOH B:176 , HOH B:242 , HOH B:290BINDING SITE FOR RESIDUE NA B 154
07AC7SOFTWAREGLY B:80 , ALA B:148 , SER B:150 , HOH B:163 , HOH B:167BINDING SITE FOR RESIDUE NA B 155
08AC8SOFTWAREHIS B:106 , SER B:108 , HOH B:196 , HOH B:259 , HOH B:343BINDING SITE FOR RESIDUE NA B 156
09AC9SOFTWAREPRO B:32 , ASP B:34 , ASP B:94 , HOH B:184 , HOH B:331BINDING SITE FOR RESIDUE NA B 157
10BC1SOFTWAREARG B:82 , VAL B:83 , GLU B:84 , ALA B:104 , LEU B:107 , HOH B:173BINDING SITE FOR RESIDUE EDO B 158
11BC2SOFTWAREMET A:73 , GLN B:65 , HOH B:341BINDING SITE FOR RESIDUE EDO B 159

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TYP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:108 -Pro A:109
2Ser B:108 -Pro B:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TYP)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTHPS51707 CYTH domain profile.3PASE_NITEU1-148  1B:3-149

(-) Exons   (0, 0)

(no "Exon" information available for 3TYP)

(-) 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:146
 aligned with 3PASE_NITEU | Q82UI9 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:150
                                                                                                                                                                              151 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        |-
          3PASE_NITEU     3 EIERKFLVATFPDGELHAVPLRQGYLTTPTDSIELRLRQQGTEYFMTLKSEGGLSRQEYEIQIDVTQFEMLWPATEGRRVEKTRYSGKLPDGQLFELDVFAGHLSPLMLVEVEFLSEDAAQAFIPPPWFGEEVTEDKRYKNKALALSIP-   -
               SCOP domains d3typa_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee........eeeeeeeee........eeeeeee..eeeeeeee.----.eeeeeeehhhhhhhhhhhhh..eeeeeeeeee.....eeeeeee.hhhh..eeeeee..hhhhhhhh.....eeee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CYTH  PDB: - UniProt: 1-148                                                                                                                       ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3typ A   4 EIERKFLVATFPDGELHAVPLRQGYLTTPTDSIELRLRQQGTEYFMTLKSE----RQEYEIQIDVTQFEMLWPATEGRRVEKTRYSGKLPDGQLFELDVFAGHLSPLMLVEVEFLSEDAAQAFIPPPWFGEEVTEDKRYKNKALALSIPG 153
                                    13        23        33        43        53|    |  63        73        83        93       103       113       123       133       143       153
                                                                             54   59                                                                                              


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with 3PASE_NITEU | Q82UI9 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:155
                               1                                                                                                                                                   151 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147   | 
          3PASE_NITEU     - ---MTEIERKFLVATFPDGELHAVPLRQGYLTTPTDSIELRLRQQGTEYFMTLKSEGGLSRQEYEIQIDVTQFEMLWPATEGRRVEKTRYSGKLPDGQLFELDVFAGHLSPLMLVEVEFLSEDAAQAFIPPPWFGEEVTEDKRYKNKALALSIP-   -
               SCOP domains d3typb_ B: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeeeee........eeeeeee..eeeeeee..-----.eeeeeehhhhhhhhhhhhh..eeeeeeeeee.....eeeeeee.hhhh..eeeeeee...hhhhhh.....eeee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CYTH  PDB: B:3-149 UniProt: 1-148                                                                                                                   ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3typ B  -1 GHMVTEIERKFLVATFPDGELHAVPLRQGYLTTPTDSIELRLRQQGTEYFMTLKSE-----QEYEIQIDVTQFEMLWPATEGRRVEKTRYSGKLPDGQLFELDVFAGHLSPLMLVEVEFLSEDAAQAFIPPPWFGEEVTEDKRYKNKALALSIPG 153
                                     8        18        28        38        48     |   - |      68        78        88        98       108       118       128       138       148     
                                                                                  54    60
   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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TYP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TYP)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (3PASE_NITEU | Q82UI9)
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:0050355    triphosphatase activity    Catalysis of the reaction: H(2)O + triphosphate = diphosphate + phosphate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        3PASE_NITEU | Q82UI9: 2fbl

(-) Related Entries Specified in the PDB File

2fbl 2FBL HAS SEQUENCE ERRORS