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(-) Description

Title :  METHYLATED SHIGELLA FLEXNERI MXIC
 
Authors :  J. E. Deane, P. Roversi, C. King, S. Johnson, S. M. Lea
Date :  06 Dec 07  (Deposition) - 11 Mar 08  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Secretion Regulation, Transport Protein, T3Ss, Virulence, Transport, 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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    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

  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, 40)

Asymmetric Unit (1, 40)
No.NameCountTypeFull Name
1MLY40Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MLY20Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1MLY20Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2VJ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VJ4)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Ser A:64 -Gly A:65
2Arg A:69 -Gly A:70
3Gly A:70 -Ser A:71
4Thr A:96 -Leu A:97
5Pro A:102 -Leu A:103
6Asp A:133 -Leu A:134
7Thr A:135 -Ala A:136
8Ser A:354 -Arg A:355
9Ser B:64 -Gly B:65
10Arg B:69 -Gly B:70
11Gly B:70 -Ser B:71
12Thr B:96 -Leu B:97
13Pro B:102 -Leu B:103
14Asp B:133 -Leu B:134
15Thr B:135 -Ala B:136
16Ser B:354 -Arg B:355

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 2VJ4)

(-) 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:292
 aligned with MXIC_SHIFL | Q04640 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:319
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
           MXIC_SHIFL    37 SGLANSKYIDSSDEMASALSSFINRRDLEKLKGTNSDSQERILDGEEDEINHKIFDLKRTLKDNLPLDRDFIDRLKRYFKDPSDQVLALRELLNEKDLTAEQVELLTKIINEIISGSEKSVNAGINSAIQAKLFGNKMKLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEKPSCNAYEFGFVLSKLIAIKMIRTSDVIFMKKLESSSLLKDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFKSESEREIAINILRELVTSAYKKELSR 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--------------------------.....-hhhhh...hhhhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vj4 A  64 SGLVP--------------------------RGSHM-SQERILDGEEDEINHkIFDLkRTLkDNLPLDRDFIDRLkRYFkDPSDQVLALRELLNEkDLTAEQVELLTkIINEIISGSEkSVNAGINSAIQAkLFGNkMkLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEkPSCNAYEFGFVLSkLIAIkMIRTSDVIFMkkLESSSLLkDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFkSESEREIAINILRELVTSAYkkELSR 355
                                |    -         -         - |   | |76        86  |    |96 |     106     | 116       126     | 136       146       156       166 |    |176       186       196       206       216       226   |   236       246  |    256   ||  266  |    276       286       296       306       316       326  |    336       346   ||    
                               68                         69  73 |             89-MLY|   |           112-MLY             132-MLY     144-MLY    155-MLY      168-MLY| |                                                    230-MLY       244-MLY|        260-MLY  269-MLY                                                     329-MLY              350-MLY 
                                                                74                  94-MLY               116-MLY                                                  173-MLY                                                                     249-MLY     261-MLY                                                                                   351-MLY
                                                                                        98-MLY                                                                      175-MLY                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with MXIC_SHIFL | Q04640 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:319
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
           MXIC_SHIFL    37 SGLANSKYIDSSDEMASALSSFINRRDLEKLKGTNSDSQERILDGEEDEINHKIFDLKRTLKDNLPLDRDFIDRLKRYFKDPSDQVLALRELLNEKDLTAEQVELLTKIINEIISGSEKSVNAGINSAIQAKLFGNKMKLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEKPSCNAYEFGFVLSKLIAIKMIRTSDVIFMKKLESSSLLKDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFKSESEREIAINILRELVTSAYKKELSR 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------HrpJ-2vj4B01 B:74-206                                                                                                                ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------HrpJ-2vj4B02 B:74-206                                                                                                                ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....--------------------------.....-hhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vj4 B  64 SGLVP--------------------------RGSHM-SQERILDGEEDEINHkIFDLkRTLkDNLPLDRDFIDRLkRYFkDPSDQVLALRELLNEkDLTAEQVELLTkIINEIISGSEkSVNAGINSAIQAkLFGNkMkLEPQLLRACYRGFIMGNISTTDQYIEWLGNFGFNHRHTIVNFVEQSLIVDMDSEkPSCNAYEFGFVLSkLIAIkMIRTSDVIFMkkLESSSLLkDGSLSAEQLLLTLLYIFQYPSESEQILTSVIEVSRASHEDSVVYQTYLSSVNESPHDIFkSESEREIAINILRELVTSAYkkELSR 355
                                |    -         -         - |   | |76        86  |    |96 |     106     | 116       126     | 136       146       156       166 |    |176       186       196       206       216       226   |   236       246  |    256   ||  266  |    276       286       296       306       316       326  |    336       346   ||    
                               68                         69  73 |             89-MLY|   |           112-MLY             132-MLY     144-MLY    155-MLY      168-MLY| |                                                    230-MLY       244-MLY|        260-MLY  269-MLY                                                     329-MLY              350-MLY 
                                                                74                  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 2VJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VJ4)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: HrpJ] (5)
(-)
Family: HrpJ (5)
(-)
Shigella flexneri (3)
1aHrpJ-2vj4B01B:74-206
1bHrpJ-2vj4B02B:74-206

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  Cis Peptide Bonds
    Arg A:69 - Gly A:70   [ RasMol ]  
    Arg B:69 - Gly B:70   [ RasMol ]  
    Asp A:133 - Leu A:134   [ RasMol ]  
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  2vj4
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2vix METHYLATED SHIGELLA FLEXNERI MXIC
2vj5 SHIGELLA FLEXNERI MXIC