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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN.
 
Authors :  G. Minasov, J. S. Brunzelle, L. Shuvalova, D. J. Miller, F. R. Collart, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Gen (Mcsg)
Date :  14 Oct 05  (Deposition) - 29 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Ykui Protein, Eal Domain, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, S. Padavattan, L. Shuvalova, J. S. Brunzelle, D. J. Miller A. Basle, C. Massa, F. R. Collart, T. Schirmer, W. F. Anderson
Crystal Structures Of Ykui And Its Complex With Second Messenger Cyclic Di-Gmp Suggest Catalytic Mechanism Of Phosphodiester Bond Cleavage By Eal Domains.
J. Biol. Chem. V. 284 13174 2009
PubMed-ID: 19244251  |  Reference-DOI: 10.1074/JBC.M808221200

(-) Compounds

Molecule 1 - YKUI PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YKUI
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:308 , TYR A:399BINDING SITE FOR RESIDUE BME A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BAS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BAS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BAS)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EALPS50883 EAL domain profile.YKUI_BACSU1-250  1B:1-250

(-) Exons   (0, 0)

(no "Exon" information available for 2BAS)

(-) 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:402
 aligned with YKUI_BACSU | O35014 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:406
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401      
           YKUI_BACSU     2 LDPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLDAGIPEEYKLEVDNRIIRQALDRFLEADSDLLIFMNQDANLLMLDHGESFLELLKEYEAKGIELHRFVLEITEHNFEGDIEQLYHMLAYYRTYGIKIAVDNIGKESSNLDRIALLSPDLLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYLVSPSETFLERDVLKQRLKTEFHQFITHEKKKLETVYEHSEQFYKRVHQAVTSLRKNNLSSDDDFIKKLAEELTDCSFRIYMCDEEGDQLTGNVFKQDGEWIYQPEYAEKNWSWRPYFLENIMRMRNLRKGFFSDLYSDLETGEMIRTFSYPMDDQMYLFIDLPYSYLYEQDGLI 407
               SCOP domains d2basa1 A:2-262 Hypothetical protein YkuI, N-terminal domain                                                                                                                                                                                                         d2basa2 A:263-407 Hypothetical protein YkuI, C-terminal domain                                                                                    SCOP domains
               CATH domains 2basA01 A:2-229 EAL domain-like                                                                                                                                                                                                     ----------------2basA02 A:246-291                             2basA03 A:292-407  [code=3.30.450.20, no name defined]                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeeeeeeee.....eeeeeeeeeeee..eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee.......hhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhh..eeeee.....----.hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh.eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeee........eeeee..eeeeehhhh........hhhhhhhhhhhhh..ee...ee......eeeeeeeee...eeeeeeehhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE EAL  PDB: - UniProt: 1-250                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bas A   2 LDPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLDAGIPEEYKLEVDNRIIRQALDRFLEADSDLLIFmNQDANLLmLDHGESFLELLKEYEAKGIELHRFVLEITEHNFEGDIEQLYHmLAYYRTYGIKIAVDNIGKESSNLDRIALLSPDLLKIDLQALK----SPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYLVSPSETFLERDVLKQRLKTEFHQFITHEKKKLETVYEHSEQFYKRVHQAVTSLRKNNLSSDDDFIKKLAEELTDCSFRIYmCDEEGDQLTGNVFKQDGEWIYQPEYAEKNWSWRPYFLENImRmRNLRKGFFSDLYSDLETGEmIRTFSYPmDDQmYLFIDLPYSYLYEQDGLI 407
                                    11        21        31        41        51        61        71        81     |  91   |   101       111       121       131      |141       151       161       171        |-   |   191       201       211       221       231       241       251       261       271       281       291       301       311  |    321       331       341       351   | | 361       371     | 381   |   391       401      
                                                                                                                87-MSE  95-MSE                                    138-MSE                                   180  185                                                                                                                              314-MSE                                  355-MSE               377-MSE 385-MSE                  
                                                                                                                                                                                                                                                                                                                                                                                             357-MSE                         389-MSE              


Chain B from PDB  Type:PROTEIN  Length:397
 aligned with YKUI_BACSU | O35014 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:401
                             1                                                                                                                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 
           YKUI_BACSU     - -MLDPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLDAGIPEEYKLEVDNRIIRQALDRFLEADSDLLIFMNQDANLLMLDHGESFLELLKEYEAKGIELHRFVLEITEHNFEGDIEQLYHMLAYYRTYGIKIAVDNIGKESSNLDRIALLSPDLLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYLVSPSETFLERDVLKQRLKTEFHQFITHEKKKLETVYEHSEQFYKRVHQAVTSLRKNNLSSDDDFIKKLAEELTDCSFRIYMCDEEGDQLTGNVFKQDGEWIYQPEYAEKNWSWRPYFLENIMRMRNLRKGFFSDLYSDLETGEMIRTFSYPMDDQMYLFIDLPYSYL 400
               SCOP domains d2basb1 B:0-262 Hypothetical protein YkuI, N-terminal domain                                                                                                                                                                                                           d2basb2 B:263-400 Hypothetical protein YkuI, C-terminal domain                                                                             SCOP domains
               CATH domains 2basB01 B:0-229 EAL domain-like                                                                                                                                                                                                       ----------------2basB02 B:246-291                             2basB03 B:292-400  [code=3.30.450.20, no name defined]                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeeeee.....eeeeeeeeeeee..eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.......hhhhhhhhhhhhhh...eeee........hhhhhhhhh..eeeee.....----..hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhh..eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeeeee...ee...eeee....eeeehhhh.ee.....hhhhhhhhhhhhh..ee...ee......eeeeeeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -EAL  PDB: B:1-250 UniProt: 1-250                                                                                                                                                                                                                          ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bas B   0 AmLDPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLDAGIPEEYKLEVDNRIIRQALDRFLEADSDLLIFmNQDANLLmLDHGESFLELLKEYEAKGIELHRFVLEITEHNFEGDIEQLYHmLAYYRTYGIKIAVDNIGKESSNLDRIALLSPDLLKIDLQALK----SPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYLVSPSETFLERDVLKQRLKTEFHQFITHEKKKLETVYEHSEQFYKRVHQAVTSLRKNNLSSDDDFIKKLAEELTDCSFRIYmCDEEGDQLTGNVFKQDGEWIYQPEYAEKNWSWRPYFLENImRmRNLRKGFFSDLYSDLETGEmIRTFSYPmDDQmYLFIDLPYSYL 400
                             |       9        19        29        39        49        59        69        79       |89     |  99       109       119       129       139       149       159       169       179|    | 189       199       209       219       229       239       249       259       269       279       289       299       309    |  319       329       339       349     | 359       369       379     | 389       399 
                             1-MSE                                                                                87-MSE  95-MSE                                    138-MSE                                   180  185                                                                                                                              314-MSE                                  355-MSE               377-MSE 385-MSE           
                                                                                                                                                                                                                                                                                                                                                                                               357-MSE                         389-MSE
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BAS)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2BAS)

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  2bas
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 Related Entries

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UniProtKB/Swiss-Prot
        YKUI_BACSU | O35014: 2w27

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