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(-) Description

Title :  CRYSTAL STRUCTURE OF A POSSIBLE TRANSCIPTIONAL REGULATOR YGGD FROM SHIGELLA FLEXNERI 2A STR. 2457T
 
Authors :  K. Tan, M. Borovilos, S. Clancy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  12 Feb 08  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D  (2x)
Keywords :  Apc27974, Yggd, Mannitol Operon Repressor, Shigella Flexneri 2A Str. 2457T, Methylation, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, S. Clancy, M. Borovilos, M. Zhou, S. Horer, S. Moy, L. L. Volkart J. Sassoon, U. Baumann, A. Joachimiak
The Mannitol Operon Repressor Mtlr Belongs To A New Class O Transcription Regulators In Bacteria.
J. Biol. Chem. V. 284 36670 2009
PubMed-ID: 19840941  |  Reference-DOI: 10.1074/JBC.M109.062679

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR
    Atcc: 700930
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YGGD, S3120, SF2919
    Organism Scientific: SHIGELLA FLEXNERI 2A STR. 2457T
    Organism Taxid: 198215
    Strain: 2457T / SEROTYPE 2A
 
Molecule 2 - PUTATIVE TRANSCRIPTIONAL REGULATOR
    Atcc: 700930
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YGGD, S3120, SF2919
    Organism Scientific: SHIGELLA FLEXNERI 2A STR. 2457T
    Organism Taxid: 198215
    Strain: 2457T / SEROTYPE 2A
 
Molecule 3 - PUTATIVE TRANSCRIPTIONAL REGULATOR
    Atcc: 700930
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YGGD, S3120, SF2919
    Organism Scientific: SHIGELLA FLEXNERI 2A STR. 2457T
    Organism Taxid: 198215
    Strain: 2457T / SEROTYPE 2A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A   
Biological Unit 2 (1x):  BC 
Biological Unit 3 (2x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 41)

Asymmetric Unit (3, 41)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MLY22Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 21)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 16)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , ASN D:18BINDING SITE FOR RESIDUE ACT A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C8G)

(-) Exons   (0, 0)

(no "Exon" information available for 3C8G)

(-) 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:166
 aligned with FUME_SHIFL | Q83Q96 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
           FUME_SHIFL     - -MATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 168
               SCOP domains -d3c8ga1 A:1-168 Putative transcriptional regulator YggD                                                                                                                  SCOP domains
               CATH domains 3c8gA00 A:0-168 Nucleotidyltransferases  domain 2                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8g A   0 AmATLTEDDVLEQLDAQDNLFSFmkTAHSILLQGIRQFLPSLFVDNDEEIVEYAVkPLLAQSGPLDDIDVALRLIYALGkmDkWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALkAmkFA---VWSEARFSGmVKTALTLAVTTTLKELT 168
                             |       9        19   ||   29        39        49     |  59        69        79| |     89        99       109       119       129   | || |-  |    149 |     159         
                             |                    23-MSE                          55-MLY                  79-MLY                                               133-MLY| 142      151-MSE             
                             1-MSE                 24-MLY                                                  80-MSE                                                135-MSE                             
                                                                                                             82-MLY                                               136-MLY                            
                                                                                                                                                                    138                              


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d3c8gb1 B:3-168 Putative transcriptional regulator YggD                                                                                                                SCOP domains
               CATH domains 3c8gB00 B:3-168 Nucleotidyltransferases  domain 2                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8g B   3 TLTEDDVLEQLDAQDNLFSFmkTAHSILLQGIRQFLPSLFVDNDEEIVEYAVkPLLAQSGPLDDIDVALRLIYALGKmDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALkAmkFADFAVWSEARFSGmVkTALTLAVTTTLkELT 168
                                    12        22||      32        42        52  |     62        72       |82        92       102       112       122       132| ||   142       152|      162  |   
                                               23-MSE                          55-MLY                   80-MSE                                              133-MLY           151-MSE       165-MLY
                                                24-MLY                                                                                                        135-MSE           153-MLY           
                                                                                                                                                               136-MLY                            


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with FUME_SHIFL | Q83Q96 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
           FUME_SHIFL     - -MATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 168
               SCOP domains d3c8gc_ C: Putative transcriptional regulator YggD                                                                                                                        SCOP domains
               CATH domains 3c8gC00 C:0-168 Nucleotidyltransferases  domain 2                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..--..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8g C   0 AmATLTEDDVLEQLDAQDNLFSFmkTAHSILLQGIRQFLPSLFVDNDEEIVEYAVkPLLAQSGPLDDIDVALRLIYALGkmDkWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALkAmkFAD--VWSEARFSGmVKTALTLAVTTTLKELT 168
                             |       9        19   ||   29        39        49     |  59        69        79| |     89        99       109       119       129   | ||139  |    149 |     159         
                             1-MSE                23-MSE                          55-MLY                  79-MLY                                               133-MLY |  |      151-MSE             
                                                   24-MLY                                                  80-MSE                                                135-MSE  |                          
                                                                                                             82-MLY                                               136-MLY |                          
                                                                                                                                                                     139  |                          
                                                                                                                                                                        142                          


Chain D from PDB  Type:PROTEIN  Length:161
 aligned with FUME_SHIFL | Q83Q96 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           FUME_SHIFL     2 ATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 168
               SCOP domains d3c8gd1 D:2-168 Putative transcriptional regulator YggD                                                                                                                 SCOP domains
               CATH domains 3c8gD00 D:2-168 Nucleotidyltransferases  domain 2                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh------hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8g D   2 ATLTEDDVLEQLDAQDNLFSFmkTAHSILLQGIRQFLPSLFVDNDEEIVEYAVkPLLAQSGPLDDIDVALRLIYALGkmDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAmkFA------EARFSGmVKTALTLAVTTTLKELT 168
                                    11        21 ||     31        41        51   |    61        71       |81        91       101       111       121       131   || |  -   |   151       161       
                                                23-MSE                          55-MLY                  79-MLY                                                 135-MSE   145     |                 
                                                 24-MLY                                                  80-MSE                                                 136-MLY        151-MSE             
                                                                                                                                                                  138
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C8G)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3C8G)

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