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(-) Description

Title :  CRYSTAL STRUCTURE OF YJJV, TATD HOMOLOG FROM ESCHERICHIA COLI K12, AT 1.8 A RESOLUTION
 
Authors :  V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  14 Jun 05  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Yjjv, Escherichia Coli, Hydrolaze, Zinc, Crystal Structure, Peg, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of Yjjv, Tatd Homolog From Escherichia Coli K12, At 1. 8 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE DEOXYRIBONUCLEASE YJJV
    Chains: A
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: YJJV
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1P331Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
2ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:11 , GLU A:97 , ASP A:207 , ZN A:402 , HOH A:767BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREGLU A:97 , HIS A:133 , HIS A:157 , ZN A:401 , HOH A:767 , HOH A:791BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREASP A:117 , HIS A:144 , HIS A:148BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREMET A:1 , HOH A:553 , HOH A:848BINDING SITE FOR RESIDUE ZN A 404
5AC5SOFTWAREHIS A:66 , PRO A:67 , GLY A:68 , MET A:69 , ASP A:101 , PHE A:103 , ASP A:106 , PRO A:107 , GLN A:108 , GLN A:112 , ASP A:210 , HOH A:550 , HOH A:571 , HOH A:584 , HOH A:756BINDING SITE FOR RESIDUE P33 A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:15 -Pro A:16
2Ala A:208 -Pro A:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TATD_1PS01137 TatD deoxyribonuclease family signature 1.YJJV_ECOLI5-13  1A:5-13
2TATD_2PS01090 TatD deoxyribonuclease family signature 2.YJJV_ECOLI129-139  1A:129-139
3TATD_3PS01091 TatD deoxyribonuclease family signature 3.YJJV_ECOLI193-209  1A:193-209

(-) Exons   (0, 0)

(no "Exon" information available for 1ZZM)

(-) 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:259
 aligned with YJJV_ECOLI | P39408 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                    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         
           YJJV_ECOLI     1 MICRFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQALERRPAKVVAVGEIGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDLPRTGVVHGFSGSLQQAERFVQLGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNVP 259
               SCOP domains d1zzma1 A:1-259 Putative deoxyribonuclease YjjV                                                                                                                                                                                                                     SCOP domains
               CATH domains 1zzmA00 A:1-259 Metal-dependent hydrolases                                                                                                                                                                                                                          CATH domains
               Pfam domains -----TatD_DNase-1zzmA01 A:6-257                                                                                                                                                                                                                                  -- Pfam domains
         Sec.struct. author ....eee............hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eee.....hhhhhhhhhhh..eeeehhhhhh....hhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TATD_1   -------------------------------------------------------------------------------------------------------------------TATD_2     -----------------------------------------------------TATD_3           -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zzm A   1 MICRFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQALERRPAKVVAVGEIGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDLPRTGVVHGFSGSLQQAERFVQLGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNVP 259
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YJJV_ECOLI | P39408)
molecular function
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    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:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1xwy RELATED ID: NYSGRC-T862 RELATED DB: TARGETDB RELATED ID: NYSGXRC-T2215 RELATED DB: TARGETDB