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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF YPBH
 
Authors :  F. Wang, Z. Mei, Y. Qi, C. Yan, J. Wang, Y. Shi
Date :  14 Sep 09  (Deposition) - 29 Sep 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ypbh, Adaptor Protein, Competence, Sporulation, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, Z. Mei, Y. Qi, C. Yan, S. Xiang, Z. Zhou, Q. Hu, J. Wang, Y. Shi
Crystal Structure Of The Meca Degradation Tag
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADAPTER PROTEIN MECA 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 104-194
    Gene: YPBH
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: YPBH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1IOD14Ligand/IonIODIDE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:5 , HOH A:118 , HOH A:122BINDING SITE FOR RESIDUE IOD A 92
02AC2SOFTWAREILE A:67BINDING SITE FOR RESIDUE IOD A 93
03AC3SOFTWAREGLN A:21 , THR A:26 , GLU A:84BINDING SITE FOR RESIDUE IOD A 94
04AC4SOFTWAREGLY A:28 , GLU A:42 , HOH A:125BINDING SITE FOR RESIDUE IOD A 95
05AC5SOFTWAREHIS A:8 , ASN A:61BINDING SITE FOR RESIDUE IOD A 97
06AC6SOFTWARETYR A:37 , HOH A:129 , GLU B:11 , GLN B:15BINDING SITE FOR RESIDUE IOD A 98
07AC7SOFTWARETHR B:66BINDING SITE FOR RESIDUE IOD B 92
08AC8SOFTWAREGLU A:11 , TYR B:37BINDING SITE FOR RESIDUE IOD B 93
09AC9SOFTWAREILE B:67BINDING SITE FOR RESIDUE IOD B 94
10BC1SOFTWAREHIS B:8 , ASN B:61BINDING SITE FOR RESIDUE IOD B 95
11BC2SOFTWAREGLN B:21 , THR B:26 , GLU B:84BINDING SITE FOR RESIDUE IOD B 96
12BC3SOFTWARETHR B:48BINDING SITE FOR RESIDUE IOD B 97

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JTN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JTN)

(-) 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:89
 aligned with MECA2_BACSU | P50734 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:89
                                   114       124       134       144       154       164       174       184         
          MECA2_BACSU   105 DIIYQFHSFEDIIQLSESLQRIGITGGTVYHYDGQYFLSLEDLGSHTAEGVVAVLAEYGNPTTLTIYRLQEYGKLIMDGNAVETIQTHF 193
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh.....eeeee..eeeeee......hhhhhhhhhhhhhee...hhhhhhhhheeee..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 3jtn A   2 DIIYQFHSFEDIIQLSESLQRIGITGGTVYHYDGQYFLSLEDLGSHTAEGVVAVLAEYGNPTTLTIYRLQEYGKLIMDGNAVETIQTHF  90
                                    11        21        31        41        51        61        71        81         


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with MECA2_BACSU | P50734 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:90
                                   114       124       134       144       154       164       174       184       194
          MECA2_BACSU   105 DIIYQFHSFEDIIQLSESLQRIGITGGTVYHYDGQYFLSLEDLGSHTAEGVVAVLAEYGNPTTLTIYRLQEYGKLIMDGNAVETIQTHFS 194
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) MecA-3jtnB01 B:2-88                                                                    --- Pfam domains (1)
           Pfam domains (2) MecA-3jtnB02 B:2-88                                                                    --- Pfam domains (2)
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh.....eeeee..eeeeee......hhhhhhhhhhhhhee...hhhhhhhhheeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3jtn B   2 DIIYQFHSFEDIIQLSESLQRIGITGGTVYHYDGQYFLSLEDLGSHTAEGVVAVLAEYGNPTTLTIYRLQEYGKLIMDGNAVETIQTHFS  91
                                    11        21        31        41        51        61        71        81        91
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3JTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: MecA] (5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MECA2_BACSU | P50734)
molecular function
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0030420    establishment of competence for transformation    The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
    GO:0045808    negative regulation of establishment of competence for transformation    Any process that stops, prevents, or reduces the frequency, rate or extent of establishment of competence for transformation.
    GO:0042174    negative regulation of sporulation resulting in formation of a cellular spore    Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

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 Related Entries

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        MECA2_BACSU | P50734: 3jto

(-) Related Entries Specified in the PDB File

3jto 3jtp