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(-) Description

Title :  THE STRUCTURE OF A HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. SUBTILIS
 
Authors :  M. E. Cuff, Y. Kim, R. Zhang, A. Joachimiak, F. Collart, P. Quartey, Midwest Center For Structural Genomics (Mcsg)
Date :  25 Jan 03  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Hydrolase, Bacillus Subtilis, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, Y. Kim, R. Zhang, A. Joachimiak, F. Collart, P. Quartey
The Structure Of A Haloacid Dehalogenase-Like Hydrolase From B. Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN, HALOACID DEHALOGENASE-LIKE HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YWPJ
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , LEU A:8 , ASP A:9 , THR A:41 , GLY A:42 , ARG A:125 , LYS A:214 , ASN A:240 , CA A:903 , HOH A:914 , HOH A:929BINDING SITE FOR RESIDUE PO4 A 900
2AC2SOFTWARELYS A:211 , LYS A:282 , HIS A:283 , HOH A:938 , HOH A:1028 , HOH A:1046 , HOH A:1130 , HOH A:1318BINDING SITE FOR RESIDUE PO4 A 901
3AC3SOFTWAREASP A:7 , ASP A:9 , ASP A:237 , SER A:238 , PO4 A:900 , HOH A:915BINDING SITE FOR RESIDUE CA A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NRW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NRW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NRW)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COF_1PS01228 Hypothetical cof family signature 1.YWPJ_BACSU3-14  1A:3-14
2COF_2PS01229 Hypothetical cof family signature 2.YWPJ_BACSU235-257  1A:235-257

(-) Exons   (0, 0)

(no "Exon" information available for 1NRW)

(-) 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:285
 aligned with YWPJ_BACSU | P94592 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:285
                                    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     
           YWPJ_BACSU     1 MKLIAIDLDGTLLNSKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEPLGIKTWVISANGAVIHDPEGRLYHHETIDKKRAYDILSWLESENYYYEVFTGSAIYTPQNGRELLDVELDRFRSANPEADLSVLKQAAEVQYSQSGFAYINSFQELFEADEPIDFYNILGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHNFELSSRKASKGQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAGKGVAMGNAREDIKSIADAVTLTNDEHGVAHMMKHLL 285
               SCOP domains d1nrwa_ A: Hypothetical protein YwpJ                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nrwA01 A:2-80,A:211-285  [code=3.40.50.1000, no name defined]                 1nrwA02 A:81-210  [code=3.30.1240.10, no name defined]                                                                            1nrwA01 A:2-80,A:211-285  [code=3.40.50.1000, no name defined]              CATH domains
               Pfam domains Hydrolase-1nrwA01 A:1-249                                                                                                                                                                                                                                ------------------------------------ Pfam domains
         Sec.struct. author ..eeeee............hhhhhhhhhhhhhh..eeeee...hhhhhhhhhh......eeeehhh.eee.....eeee...hhhhhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eee..hhhhhh.......eeeeeee..hhhhhhhhhhhhh....eeee.....eeeeee...hhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --COF_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COF_2  PDB: A:235-257  ---------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nrw A   1 mKLIAIDLDGTLLNSKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVmSIFEPLGIKTWVISANGAVIHDPEGRLYHHETIDKKRAYDILSWLESENYYYEVFTGSAIYTPQNGRELLDVELDRFRSANPEADLSVLKQAAEVQYSQSGFAYINSFQELFEADEPIDFYNILGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHNFELSSRKASKGQALKRLAKQLNIPLEETAAVGDSLNDKSmLEAAGKGVAmGNAREDIKSIADAVTLTNDEHGVAHmmKHLL 285
                            |       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|    
                            |                                              49-MSE                                                                                                                                                                                            244-MSE   254-MSE                   280-MSE 
                            1-MSE                                                                                                                                                                                                                                                                                 281-MSE
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YWPJ_BACSU | P94592)
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.
    GO:0044283    small molecule biosynthetic process    The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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