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(-) Description

Title :  CRYSTAL STRUCTURE OF EFI TARGET 500140:TATD FAMILY HYDROLASE FROM PSEUDOMONAS PUTIDA
 
Authors :  J. Kim, R. Toro, B. Hillerich, R. D. Seidel, J. A. Gerlt, S. C. Almo, Enzym Function Initiative (Efi)
Date :  31 Mar 11  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kim, R. Toro, B. Hillerich, R. D. Seidel, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of Efi Target 500140:Tatd Family Hydrolas From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TATD FAMILY HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: PP2311, PP_2311
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CIT1Ligand/IonCITRIC ACID
3MSE3Mod. Amino AcidSELENOMETHIONINE
4ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:97 , HIS A:133 , HIS A:158 , CIT A:289BINDING SITE FOR RESIDUE ZN A 288
2AC2SOFTWAREHIS A:68 , HIS A:70 , GLU A:97 , ARG A:104 , HIS A:133 , ARG A:135 , HIS A:158 , ASP A:209 , TYR A:212 , ALA A:247 , ZN A:288 , HOH A:413BINDING SITE FOR RESIDUE CIT A 289
3AC3SOFTWAREHIS A:70 , ASP A:71 , ARG A:237 , HOH A:310BINDING SITE FOR RESIDUE ACT A 290

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:96 -Glu A:97
2Ala A:210 -Pro A:211
3Arg A:219 -Pro A:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RCM)

(-) 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:279
 aligned with Q88KH9_PSEPK | Q88KH9 from UniProtKB/TrEMBL  Length:265

    Alignment length:279
                                                                                                                                                                                                                                                                                                  265              
                                    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    |    -         
         Q88KH9_PSEPK     1 MQLIDIGVNLTNSSFHDQQAAIVERALEAGVTQMLLTGTSLAVSEQALELCQQLDASGAHLFATAGVHPHDAKAWDTDSERQLRLLLSEPRVRAVGECGLDFNRDFSPRPLQEKALEAQLTLAAQLRLPVFLHERDASERLLAILKDYRDHLTGAVVHCFTGEREALFAYLDLDLHIGITGWICDERRGTHLHPLVGNIPEGRLMLESDAPYLLPRSLRPKPKSGRNEPAFLPEVLREVALHRGESAEHTAAHTTATARDFFQLP--------------   -
               SCOP domains d3rcma_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---TatD_DNase-3rcmA01 A:4-263                                                                                                                                                                                                                                          ---------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhh.hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhh..hhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh..eeeehhhhhh...hhhhhhhhh......eee.....................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rcm A   1 mQLIDIGVNLTNSSFHDQQAAIVERALEAGVTQmLLTGTSLAVSEQALELCQQLDASGAHLFATAGVHPHDAKAWDTDSERQLRLLLSEPRVRAVGECGLDFNRDFSPRPLQEKALEAQLTLAAQLRLPVFLHERDASERLLAILKDYRDHLTGAVVHCFTGEREALFAYLDLDLHIGITGWICDERRGTHLHPLVGNIPEGRLmLESDAPYLLPRSLRPKPKSGRNEPAFLPEVLREVALHRGESAEHTAAHTTATARDFFQLPAENHHHWSHPQFEK 287
                            |       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       278         
                            |                               34-MSE                                                                                                                                                                    205-MSE                                                        268|          
                            1-MSE                                                                                                                                                                                                                                                                     277
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q88KH9_PSEPK | Q88KH9)
molecular function
    GO:0016888    endodeoxyribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

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