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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE HAD FAMILY HYDROLASE FROM PSEUDOMONAS FLUORESCENS PF-5 WITH BOUND MG
 
Authors :  M. W. Vetting, Y. Patskovsky, R. Toro, J. Freeman, S. Miller, J. M. Saude S. K. Burley, D. Dunaway-Mariano, K. N. Allen, J. A. Gerlt, S. C. Almo, E Function Initiative (Efi), New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  07 Mar 11  (Deposition) - 20 Apr 11  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Enzyme Function Intitiative, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Haloalkane Dehalogenase Family, Possible Hydrolase, Enzyme Function Initiative, Efi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, Y. Patskovsky, R. Toro, J. Freeman, S. Miller, J. M. Sauder, S. K. Burley, D. Dunaway-Mariano, K. N. Allen, J. A. Gerlt S. C. Almo
Crystal Structure Of Probable Had Family Hydrolase From Pseudomonas Fluorescens Pf-5 With Bound Mg
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: PF-5, PFL_5400
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 220664
    Strain: PF-5 / ATCC BAA-477
    Synonym: PUTATIVE HAD FAMILY HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ASP A:14 , ASP A:152 , ASP A:156 , HOH A:314 , HOH A:342 , HOH A:343BINDING SITE FOR RESIDUE MG A 206
2AC2SOFTWAREHIS A:8 , ARG A:146 , HOH A:219BINDING SITE FOR RESIDUE SO4 A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R09)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:127 -Pro A:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R09)

(-) Exons   (0, 0)

(no "Exon" information available for 3R09)

(-) 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:197
 aligned with Q4K5L5_PSEF5 | Q4K5L5 from UniProtKB/TrEMBL  Length:197

    Alignment length:197
                                                                                                                                                                                                                             197 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     | 
         Q4K5L5_PSEF5     2 SLSEIKHWVFDMDGTLTIAVHDFAAIREALSIPAEDDILTHLAALPADESAAKHAWLLEHERDLAQGSRPAPGAVELVRELAGRGYRLGILTRNARELAHVTLEAIGLADCFAEADVLGRDEAPPKPHPGGLLKLAEAWDVSPSRMVMVGDYRFDLDCGRAAGTRTVLVNLPDNPWPELTDWHARDCAQLRDLLSA-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------HAD_2-3r09A01 A:19-170                                                                                                                                  ---------------------------- Pfam domains
         Sec.struct. author hhhhh.eeee......eeeeehhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..hhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.hhhhhhhh.ee..........hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee......hhhhh.eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r09 A   2 SLSEIKHWVFDmDGTLTIAVHDFAAIREALSIPAEDDILTHLAALPADESAAKHAWLLEHERDLAQGSRPAPGAVELVRELAGRGYRLGILTRNARELAHVTLEAIGLADCFAEADVLGRDEAPPKPHPGGLLKLAEAWDVSPSRmVmVGDYRFDLDCGRAAGTRTVLVNLPDNPWPELTDWHARDCAQLRDLLSAE 198
                                    11 |      21        31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181       191       
                                      13-MSE                                                                                                                               147-MSE                                               
                                                                                                                                                                             149-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 3R09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R09)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q4K5L5_PSEF5 | Q4K5L5)
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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        Q4K5L5_PSEF5 | Q4K5L5: 2ybd 3m9l

(-) Related Entries Specified in the PDB File

3m9l SAME PROTEIN WITHOUT MG BOUND RELATED ID: NYSGXRC-22261A RELATED DB: TARGETDB