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(-) Description

Title :  CRYSTAL STRUCTURE OF MANNITOL OPERON REPRESSOR (MTLR) FROM VIBRIO PARAHAEMOLYTICUS RIMD 2210633
 
Authors :  K. Tan, M. Zhou, S. Moy, A. Joachimiak, Midwest Center For Structura Genomics (Mcsg)
Date :  21 Dec 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Apc85967. 1, Mannitol Operon Repressor, Mtlr, Vibrio Parahaemolyticus Rimd 2210633, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (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 - MANNITOL OPERON REPRESSOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: VP0368
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS RIMD 2210633
    Organism Taxid: 223926

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU C:67 , LYS C:95BINDING SITE FOR RESIDUE EDO C 173
2AC2SOFTWAREVAL D:28 , LYS D:95BINDING SITE FOR RESIDUE EDO D 173
3AC3SOFTWAREASP A:66 , LEU A:67BINDING SITE FOR RESIDUE EDO A 173
4AC4SOFTWAREVAL B:28 , ILE B:92 , LYS B:95 , ASN B:96BINDING SITE FOR RESIDUE EDO B 173
5AC5SOFTWAREARG B:150 , GLN B:153 , SER B:157 , ARG D:150 , GLN D:153 , ILE D:154 , SER D:157BINDING SITE FOR RESIDUE GOL B 174

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:134 -Pro A:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BRJ)

(-) 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:167
 aligned with Q87SQ4_VIBPA | Q87SQ4 from UniProtKB/TrEMBL  Length:176

    Alignment length:167
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       
         Q87SQ4_VIBPA     6 NESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKMGMVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
               SCOP domains d3brja1 A:6-172 Mannitol operon repressor MtlR                                                                                                                          SCOP domains
               CATH domains 3brjA00 A:6-172 Nucleotidyltransferases  domain 2                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.hhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brj A   6 NESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKmGmVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
                                    15        25        35        45        55        65        75        85        95       105       115       125 |     135       145       155       165       
                                                                                                                                                 125-MSE                                           
                                                                                                                                                   127-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:169
 aligned with Q87SQ4_VIBPA | Q87SQ4 from UniProtKB/TrEMBL  Length:176

    Alignment length:169
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163         
         Q87SQ4_VIBPA     4 NINESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKMGMVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
               SCOP domains d3brjb_ B: Mannitol operon repressor MtlR                                                                                                                                 SCOP domains
               CATH domains 3brjB00 B:4-172 Nucleotidyltransferases  domain 2                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brj B   4 NINESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKmGmVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
                                    13        23        33        43        53        63        73        83        93       103       113       123 | |   133       143       153       163         
                                                                                                                                                   125-MSE                                           
                                                                                                                                                     127-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:163
 aligned with Q87SQ4_VIBPA | Q87SQ4 from UniProtKB/TrEMBL  Length:176

    Alignment length:167
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       
         Q87SQ4_VIBPA     6 NESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKMGMVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
               SCOP domains d3brjc_ C: Mannitol operon repressor MtlR                                                                                                                               SCOP domains
               CATH domains 3brjC00 C:6-172 Nucleotidyltransferases  domain 2                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.........----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brj C   6 NESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKmGmVQLEVN----DIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
                                    15        25        35        45        55        65        75        85        95       105       115       125 |     | -  |    145       155       165       
                                                                                                                                                 125-MSE 133  138                                  
                                                                                                                                                   127-MSE                                         


Chain D from PDB  Type:PROTEIN  Length:168
 aligned with Q87SQ4_VIBPA | Q87SQ4 from UniProtKB/TrEMBL  Length:176

    Alignment length:168
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164        
         Q87SQ4_VIBPA     5 INESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKMGMVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
               SCOP domains d3brjd_ D: Mannitol operon repressor MtlR                                                                                                                                SCOP domains
               CATH domains 3brjD00 D:5-172 Nucleotidyltransferases  domain 2                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3brj D   5 INESEIIERLNSAPSVRGFFIATVDVFNESIDGLIQRIFRKDNFAVQSVVGPLLQDSGPLGDLSVRLKLLFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHLVKKmGmVQLEVNEPDDDIDLEFYQLQLQRQQQIIKSGLSLAIVEICNELGK 172
                                    14        24        34        44        54        64        74        84        94       104       114       124| |    134       144       154       164        
                                                                                                                                                  125-MSE                                           
                                                                                                                                                    127-MSE
   Legend:   → Mismatch (orange background)
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    → 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 3BRJ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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