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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE HAD FAMILY HYDROLASE FROM PSEUDOMONAS FLUORESCENS PF-5 WITH BOUND PHOSPHATE
 
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
Date :  03 Mar 11  (Deposition) - 16 Mar 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Psi (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 Phosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS FLUORESCENS PF-5
    Organism Taxid: 220664

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ASP A:14 , HIS A:61 , ASP A:152 , PO4 A:1199BINDING SITE FOR RESIDUE MG A 1198
2AC2SOFTWAREASP A:12 , MSE A:13 , ASP A:14 , THR A:93 , ARG A:94 , LYS A:127 , MG A:1198BINDING SITE FOR RESIDUE PO4 A 1199
3AC3SOFTWAREHIS A:8 , ARG A:146 , HOH A:2176BINDING SITE FOR RESIDUE PO4 A 1200

(-) SS Bonds  (0, 0)

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

(-) 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 2YBD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YBD)

(-) 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:196
 aligned with Q4K5L5_PSEF5 | Q4K5L5 from UniProtKB/TrEMBL  Length:197

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
         Q4K5L5_PSEF5     2 SLSEIKHWVFDMDGTLTIAVHDFAAIREALSIPAEDDILTHLAALPADESAAKHAWLLEHERDLAQGSRPAPGAVELVRELAGRGYRLGILTRNARELAHVTLEAIGLADCFAEADVLGRDEAPPKPHPGGLLKLAEAWDVSPSRMVMVGDYRFDLDCGRAAGTRTVLVNLPDNPWPELTDWHARDCAQLRDLLSA 197
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------HAD_2-2ybdA01 A:19-170                                                                                                                                  --------------------------- Pfam domains
         Sec.struct. author hhhhh.eeee......eeeeehhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..hhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.hhhhhhhh.ee..........hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeee.......hhhhh.ee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybd A   2 SLSEIKHWVFDmDGTLTIAVHDFAAIREALSIPAEDDILTHLAALPADESAAKHAWLLEHERDLAQGSRPAPGAVELVRELAGRGYRLGILTRNARELAHVTLEAIGLADCFAEADVLGRDEAPPKPHPGGLLKLAEAWDVSPSRmVmVGDYRFDLDCGRAAGTRTVLVNLPDNPWPELTDWHARDCAQLRDLLSA 197
                                    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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  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 2YBD)

(-) CATH Domains  (0, 0)

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

(-) 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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