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(-) Description

Title :  YDCE PROTEIN FROM BACILLUS SUBTILIS
 
Authors :  A. Gogos, H. Mu, F. Bahna, C. A. Gomez, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Dec 02  (Deposition) - 14 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Conserved Hypothetical Protein Ydce, Structural Genomics, New York Sgx Research Center For Structural Genomics, Psi, Protein Structure Initiative, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gogos, H. Mu, F. Bahna, C. A. Gomez, L. Shapiro
Crystal Structure Of Ydce Protein From Bacillus Subtilis
Proteins: V. 53 320 2003 Struct. , Funct. , Genet.
PubMed-ID: 14517982  |  Reference-DOI: 10.1002/PROT.10457
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN YDCE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YDCE
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11PG2Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2ACY2Ligand/IonACETIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
11PG4Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2ACY4Ligand/IonACETIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:49 , GLN A:50 , ARG A:71 , GLU A:105 , GLN A:108 , ILE A:114 , ASP A:115 , PHE A:116 , HOH A:559BINDING SITE FOR RESIDUE 1PG A 501
2AC2SOFTWARESER A:14 , VAL A:17 , HOH A:585 , HOH A:601BINDING SITE FOR RESIDUE 1PG A 503
3AC3SOFTWAREPRO A:26 , PHE A:69 , GLU A:70 , ILE A:114 , HOH A:564 , HOH A:580BINDING SITE FOR RESIDUE ACY A 502
4AC4SOFTWAREPHE A:38 , LYS A:91 , ILE A:92BINDING SITE FOR RESIDUE ACY A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NE8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:14 -Pro A:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NE8)

(-) Exons   (0, 0)

(no "Exon" information available for 1NE8)

(-) 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:116
 aligned with ENDOA_BACSU | P96622 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
          ENDOA_BACSU     1 MIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALIDF 116
               SCOP domains d1ne8a_ A: PemK-like protein YdcE                                                                                    SCOP domains
               CATH domains 1ne8A00 A:1-116  [code=2.30.30.110, no name defined]                                                                 CATH domains
               Pfam domains ---PemK-1ne8A01 A:4-111                                                                                        ----- Pfam domains
         Sec.struct. author ......eeeeee...........eeeeee..hhhhhhhh.eeeeeeee..........eeeehhhhhh....eeeeeeeeeeee...eeeeeee.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1ne8 A   1 LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALIDF 116
                                    10        20        30        40        50        60        70        80        90       100       110
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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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: PemK] (4)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (ENDOA_BACSU | P96622)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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UniProtKB/Swiss-Prot
        ENDOA_BACSU | P96622: 4mdx 4me7

(-) Related Entries Specified in the PDB File

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