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(-) Description

Title :  STRUCTURE OF AN ENTEROCOCCUS FAECALIS HD DOMAIN PHOSPHOHYDROLASE
 
Authors :  I. I. Vorontsov, G. Minasov, L. Shuvalova, J. S. Brunzelle, S. Moy, F. R. A. Joachimiak, W. F. Anderson, Midwest Center For Structural Gen (Mcsg)
Date :  07 Dec 06  (Deposition) - 19 Dec 06  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hd Domain, Phosphohydrolase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Vorontsov, G. Minasov, O. Kiryukhina, J. S. Brunzelle, L. Shuvalova, W. F. Anderson
Characterization Of The Deoxynucleotide Triphosphate Triphosphohydrolase (Dntpase) Activity Of The Ef1143 Protei From Enterococcus Faecalis And Crystal Structure Of The Activator-Substrate Complex.
J. Biol. Chem. V. 286 33158 2011
PubMed-ID: 21757692  |  Reference-DOI: 10.1074/JBC.M111.250456

(-) Compounds

Molecule 1 - HD DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF-1143
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2HED1Ligand/Ion2-HYDROXYETHYL DISULFIDE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HED1Ligand/Ion2-HYDROXYETHYL DISULFIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HED-1Ligand/Ion2-HYDROXYETHYL DISULFIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , HIS A:110 , ASP A:111 , ASP A:183BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS B:66 , HIS B:110 , ASP B:111 , ASP B:183BINDING SITE FOR RESIDUE ZN B 502
3AC3SOFTWARETHR A:51 , HOH A:508BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWAREGLY B:50 , THR B:51 , TYR B:117 , HIS B:119 , THR B:120BINDING SITE FOR RESIDUE CL B 504
5AC5SOFTWAREGLN A:135 , PHE A:288 , LEU A:290 , HOH A:632BINDING SITE FOR RESIDUE HED A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O6I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:1 -Thr A:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O6I)

(-) Exons   (0, 0)

(no "Exon" information available for 2O6I)

(-) 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:436
 aligned with Q836G9_ENTFA | Q836G9 from UniProtKB/TrEMBL  Length:456

    Alignment length:453
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450   
         Q836G9_ENTFA     1 MTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQGNKKHYDLFDETYREFSSYIHNGALV 453
               SCOP domains d2o6ia1 A:1-453 Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh..hhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh.hhhhhheeee.--.......------.....eee....eeehhhhhhhhhhhhh.....eeeeehhhhhh---------.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6i A   1 MTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSS--LPYDFYR------RTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLD---------FDETYREFSSYIHNGALV 453
                                    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       330       340       350       360      |370     |   -  |    390       400       410       420     |   -     | 440       450   
                                                                                                                                                                                                                                                                                                                                                                                                        367  |   376    383                                        426       436                 
                                                                                                                                                                                                                                                                                                                                                                                                           370                                                                                   


Chain B from PDB  Type:PROTEIN  Length:430
 aligned with Q836G9_ENTFA | Q836G9 from UniProtKB/TrEMBL  Length:456

    Alignment length:456
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447      
         Q836G9_ENTFA     - ---MTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQGNKKHYDLFDETYREFSSYIHNGALV 453
               SCOP domains d2o6ib_ B: Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------HD-2o6iB01 B:63-191                                                                                                              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------HD-2o6iB02 B:63-191                                                                                                              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...---......hhhhhhh..hhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhh........ee..---.....----------...eee....eeehhhhhhhhhhh.........eeehhhhh----------.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o6i B  -2 SNAMTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPE---DLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINS---LPYDF----------QIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEML----------FDETYREFSSYIHNGALV 453
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  |   |277       287       297       307       317       327       337       347       357        |-  |   |  -       387       397       407       417       | -       437       447      
                                                                                                                                                                                                                                                                                                          270 274                                                                                         366 370 374        385                                     425        436
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O6I)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HD_PDEase (93)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q836G9_ENTFA | Q836G9)
molecular function
    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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        Q836G9_ENTFA | Q836G9: 3irh 4lrl

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