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(-) Description

Title :  METHYLATED SHIGELLA FLEXNERI MXIC
 
Authors :  J. E. Deane, P. Roversi, C. King, S. Johnson, S. M. Lea
Date :  05 Dec 07  (Deposition) - 11 Mar 08  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Transport Protein, Secretion Regulation, T3Ss, Virulence, Type Three Secretion System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Deane, P. Roversi, C. King, S. Johnson, S. M. Lea
Structures Of The Shigella Flexneri Type 3 Secretion System Protein Mxic Reveal Conformational Variability Amongst Homologues.
J. Mol. Biol. V. 377 985 2008
PubMed-ID: 18304577  |  Reference-DOI: 10.1016/J.JMB.2008.01.072

(-) Compounds

Molecule 1 - PROTEIN MXIC
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 74-355
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Other Details: THE CONSTRUCT IS A DELETION OF THE FIRST 73 RESIDUES AND WAS METHYLATED CHEMICALLY FOLLOWING WALTER ET AL, STRUCTURE 14,1617-1622 (2006)
    Strain: PWR100
    Synonym: MXIC

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 63)

Asymmetric Unit (3, 63)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MLY60Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MLY20Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 2 (2, 21)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MLY20Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 3 (1, 20)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3MLY20Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:183 , CYS B:184 , GLU B:201 , ASN B:205BINDING SITE FOR RESIDUE GOL B1356
2AC2SOFTWAREASP A:227 , MLY A:269BINDING SITE FOR RESIDUE ACT A1356
3AC3SOFTWAREGLU A:291BINDING SITE FOR RESIDUE GOL A1357

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro B:102 -Leu B:103
2Met C:190 -Gly C:191
3Ile C:300 -Glu C:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VIX)

(-) Exons   (0, 0)

(no "Exon" information available for 2VIX)

(-) 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:283
 aligned with MXIC_SHIFL | Q04640 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:283
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
           MXIC_SHIFL    73 DSQERILDGEEDEINHKIFDLKRTLKDNLPLDRDFIDRLKRYFKDPSDQVLALRELLNEKDLTAEQVELLTKIINEIISGSEKSVNAGINSAIQAKLFGNKMKLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEKPSCNAYEFGFVLSKLIAIKMIRTSDVIFMKKLESSSLLKDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFKSESEREIAINILRELVTSAYKKELSR 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vix A  73 MSQERILDGEEDEINHkIFDLkRTLkDNLPLDRDFIDRLkRYFkDPSDQVLALRELLNEkDLTAEQVELLTkIINEIISGSEkSVNAGINSAIQAkLFGNkMkLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEkPSCNAYEFGFVLSkLIAIkMIRTSDVIFMkkLESSSLLkDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFkSESEREIAINILRELVTSAYkkELSR 355
                                    82      | 92 |   | 102       112   |   122       132       142 |     152  |    162     | 172| |    182       192       202       212       222       232       242 |    |252       262      |272       282       292       302       312       322      |332       342       352   
                                           89-MLY|   |           112-MLY             132-MLY     144-MLY    155-MLY      168-MLY| |                                                    230-MLY       244-MLY|        260-MLY  269-MLY                                                     329-MLY              350-MLY 
                                                94-MLY               116-MLY                                                  173-MLY                                                                     249-MLY     261-MLY                                                                                   351-MLY
                                                    98-MLY                                                                      175-MLY                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with MXIC_SHIFL | Q04640 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:283
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
           MXIC_SHIFL    73 DSQERILDGEEDEINHKIFDLKRTLKDNLPLDRDFIDRLKRYFKDPSDQVLALRELLNEKDLTAEQVELLTKIINEIISGSEKSVNAGINSAIQAKLFGNKMKLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEKPSCNAYEFGFVLSKLIAIKMIRTSDVIFMKKLESSSLLKDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFKSESEREIAINILRELVTSAYKKELSR 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vix B  73 MSQERILDGEEDEINHkIFDLkRTLkDNLPLDRDFIDRLkRYFkDPSDQVLALRELLNEkDLTAEQVELLTkIINEIISGSEkSVNAGINSAIQAkLFGNkMkLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEkPSCNAYEFGFVLSkLIAIkMIRTSDVIFMkkLESSSLLkDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFkSESEREIAINILRELVTSAYkkELSR 355
                                    82      | 92 |   | 102       112   |   122       132       142 |     152  |    162     | 172| |    182       192       202       212       222       232       242 |    |252       262      |272       282       292       302       312       322      |332       342       352   
                                           89-MLY|   |           112-MLY             132-MLY     144-MLY    155-MLY      168-MLY| |                                                    230-MLY       244-MLY|        260-MLY  269-MLY                                                     329-MLY              350-MLY 
                                                94-MLY               116-MLY                                                  173-MLY                                                                     249-MLY     261-MLY                                                                                   351-MLY
                                                    98-MLY                                                                      175-MLY                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with MXIC_SHIFL | Q04640 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:281
                                    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 
           MXIC_SHIFL    72 SDSQERILDGEEDEINHKIFDLKRTLKDNLPLDRDFIDRLKRYFKDPSDQVLALRELLNEKDLTAEQVELLTKIINEIISGSEKSVNAGINSAIQAKLFGNKMKLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEKPSCNAYEFGFVLSKLIAIKMIRTSDVIFMKKLESSSLLKDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFKSESEREIAINILRELVTSAYKKE 352
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --HrpJ-2vixC01 C:74-206                                                                                                                -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --HrpJ-2vixC02 C:74-206                                                                                                                -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --HrpJ-2vixC03 C:74-206                                                                                                                -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vix C  72 HMSQERILDGEEDEINHkIFDLkRTLkDNLPLDRDFIDRLkRYFkDPSDQVLALRELLNEkDLTAEQVELLTkIINEIISGSEkSVNAGINSAIQAkLFGNkMkLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEkPSCNAYEFGFVLSkLIAIkMIRTSDVIFMkkLESSSLLkDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFkSESEREIAINILRELVTSAYkkE 352
                                    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 
                                            89-MLY|   |           112-MLY             132-MLY     144-MLY    155-MLY      168-MLY| |                                                    230-MLY       244-MLY|        260-MLY  269-MLY                                                     329-MLY              350-MLY
                                                 94-MLY               116-MLY                                                  173-MLY                                                                     249-MLY     261-MLY                                                                                   351-MLY
                                                     98-MLY                                                                      175-MLY
   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  (0, 0)

(no "SCOP Domain" information available for 2VIX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VIX)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: HrpJ] (5)
(-)
Family: HrpJ (5)
(-)
Shigella flexneri (3)
1aHrpJ-2vixC01C:74-206
1bHrpJ-2vixC02C:74-206
1cHrpJ-2vixC03C:74-206

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MXIC_SHIFL | Q04640)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0050709    negative regulation of protein secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0030254    protein secretion by the type III secretion system    The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
    GO:0046903    secretion    The controlled release of a substance by a cell or a tissue.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0043657    host cell    A cell within a host organism. Includes the host plasma membrane and any external encapsulating structures such as the host cell wall and cell envelope.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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  2vix
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  MXIC_SHIFL | Q04640
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MXIC_SHIFL | Q04640: 2vj4 2vj5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VIX)