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(-) Description

Title :  YCDX PROTEIN, TRINUCLEAR ZINC SITE
 
Authors :  A. Teplyakov, G. Obmolova, P. P. Khil, R. D. Camerini-Otero, G. L. Gilli
Date :  14 Jul 02  (Deposition) - 22 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Structural Genomics, Beta-Alpha-Barrel, Trinuclear Zinc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Teplyakov, G. Obmolova, P. P. Khil, A. J. Howard, R. D. Camerini-Otero, G. L. Gilliland
Crystal Structure Of The Escherichia Coli Ycdx Protein Reveals A Trinuclear Zinc Active Site
Proteins: V. 51 315 2003 Struct. , Funct. , Genet.
PubMed-ID: 12661000  |  Reference-DOI: 10.1002/PROT.10352

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YCDX
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPDEST14
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:15 , HIS A:40 , HIS A:194 , HOH A:322BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:7 , HIS A:9 , GLU A:73 , ASP A:192 , ZN A:303 , HOH A:441BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREGLU A:73 , HIS A:101 , HIS A:131 , ZN A:302 , HOH A:441BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREARG A:57BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARETYR A:2 , PHE A:214BINDING SITE FOR RESIDUE SO4 A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M68)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M68)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M68)

(-) Exons   (0, 0)

(no "Exon" information available for 1M68)

(-) 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:234
 aligned with YCDX_ECOLI | P75914 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           YCDX_ECOLI     2 YPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEINNSSFLHSRKGSEDNCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
               SCOP domains d1m68a_ A: Hypothetical protein YcdX                                                                                                                                                                                                                 SCOP domains
               CATH domains 1m68A00 A:2-245 Metal-dependent hydrolases                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.............hhhhhhhhhhhh...eeeeeee.........hhhhhhhhhh..ee..eeeeeeeeee..........hhhhhh...eeeee.........hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhh..eeeee...----------hhhhhhhhhhhhh..eeee....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m68 A   2 YPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEINNSS----------NCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         -|      181       191       201       211       221       231       241    
                                                                                                                                                                                         161        172                                                                         

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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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M68)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (YCDX_ECOLI | P75914)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0042578    phosphoric ester hydrolase activity    Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation 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.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0071978    bacterial-type flagellum-dependent swarming motility    Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YCDX_ECOLI | P759141m65 1pb0

(-) Related Entries Specified in the PDB File

1m65 YCDX PROTEIN