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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE P-NITROPHENYL PHOSPHATASE FROM BACILLUS SUBTILIS
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Alm York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  25 Oct 10  (Deposition) - 17 Nov 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi2, Nysgxrc, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Phosphatase Fold, P-Nitrophenyl Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative P-Nitrophenyl Phosphatase Fro Bacillus Subtilis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED HYDROLASE YUTF
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YUTF, BSU32290
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:14 , ASN A:46 , ASN A:47 , ASN A:148 , ASP A:150 , HOH A:270 , HOH A:345 , HOH A:358 , HOH A:426BINDING SITE FOR RESIDUE GOL A 267
2AC2SOFTWAREASP A:12 , ASP A:14 , GLY A:15 , LYS A:183 , ASP A:208 , ASN A:209 , THR A:212 , ASP A:213 , HOH A:283 , HOH A:345BINDING SITE FOR RESIDUE GOL A 268
3AC3SOFTWARELYS A:4 , THR A:5 , TYR A:6 , TYR A:9 , TYR A:257 , HIS A:261 , HIS A:262BINDING SITE FOR RESIDUE ACY A 269

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PDW)

(-) Exons   (0, 0)

(no "Exon" information available for 3PDW)

(-) 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:257
 aligned with YUTF_BACSU | O32125 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:263
                             1                                                                                                                                                                                                                                                            256      
                             |       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      |  -   
           YUTF_BACSU     - -MKTYKGYLIDLDGTMYNGTEKIEEACEFVRTLKDRGVPYLFVTNNSSRTPKQVADKLVSFDIPATEEQVFTTSMATAQHIAQQKKDASVYVIGEEGIRQAIEENGLTFGGENADFVVVGIDRSITYEKFAVGCLAIRNGARFISTNGDIAIPTERGLLPGNGSLTSVLTVSTGVQPVFIGKPESIIMEQAMRVLGTDVSETLMVGDNYATDIMAGINAGMDTLLVHTGVTKREHMTDDMEKPTHAIDSLTEWIPYI------   -
               SCOP domains d3pdwa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Hydrolase-3pdwA01 A:6-221                                                                                                                                                                                               ------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh...eeeee.hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhh..eeee.....eeee..eeeehhhhhhhhhhhhhh...ee.....hhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhh.eeeee...------.........eee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdw A   2 SLKTYKGYLIDLDGTMYNGTEKIEEACEFVRTLKDRGVPYLFVTNNSSRTPKQVADKLVSFDIPATEEQVFTTSMATAQHIAQQKKDASVYVIGEEGIRQAIEENGLTFGGENADFVVVGIDRSITYEKFAVGCLAIRNGARFISTNGDIAIPTERGLLPGNGSLTSVLTVSTGVQPVFIGKPESIIMEQAMRVLGTDVSETLMVGDNYATDIMAGINAGMDTLLVHTG------MTDDMEKPTHAIDSLTEWIPYIEGHHHH 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-     | 241       251       261   
                                                                                                                                                                                                                                                              230    237
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YUTF_BACSU | O32125)
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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

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