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(-) Description

Title :  PERIPLASMIC DOMAIN OF THE CHIMERIC WZZB CHAIN LENGTH REGULATOR PROTEIN
 
Authors :  S. Kalynych, D. Yao, J. D. Magee, M. Cygler
Date :  07 Mar 12  (Deposition) - 28 Mar 12  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Wzz, Regulation Of Lps O-Antigen Chain Length, Inner Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kalynych, D. Yao, J. Magee, M. Cygler
Structural Characterization Of Closely Related O-Antigen Lipopolysaccharide (Lps) Chain Length Regulators.
J. Biol. Chem. V. 287 15696 2012
PubMed-ID: 22437828  |  Reference-DOI: 10.1074/JBC.M112.354837

(-) Compounds

Molecule 1 - CHIMERIC WZZB CHAIN LENGTH DETERMINANT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFO4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PERIPLASMIC DOMAIN
    Gene: CLD, ROL, S2210, SF2089, WZZB, STM2079
    Organism Scientific: SHIGELLA FLEXNERI, SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / ATCC 700720)
    Organism Taxid: 623, 99287
    Synonym: POLYSACCHARIDE ANTIGEN CHAIN REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4E29)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E29)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E29)

(-) Exons   (0, 0)

(no "Exon" information available for 4E29)

(-) 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:233
 aligned with WZZB_SALTY | Q04866 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:237
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       
           WZZB_SALTY    55 KWTSTAIITQPDAAQVATYTNALNVLYGGNAPKISEVQANFISRFSSAFSALSEVLDNQKEREKLTIEQSVKGQALPLSVSYVSTTAEGAQRRLAEYIQQVDEEVAKELEVDLKDNITLQTKTLQESLETQEVVAQEQKDLRIKQIEEALRYADEAKITQPQIQQTQDVTQDTMFLLGSDALKSMIQNEATRPLVFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVMKPTLPVRRDS 291
               SCOP domains d4e29a_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...----.eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e29 A  55 KWTSTAIITQPDVGQIAGYNNAmNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPSVK----PLTVSYVGQTAEGAQmKLAQYIQQVDDKVNQELERDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIEEALRYADEAKITQPQIQQTQDVTQDTmFLLGSDALKSmIQNEATRPLAFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVmKPTLPVRRDS 291
                                    64        74  |     84        94       104       114       124 |    |134       144 |     154       164       174       184       194       204       214       224   |   234    |  244       254       264       274      |284       
                                                 77-MSE                                          126  131            146-MSE                                                                           228-MSE    239-MSE                                   281-MSE      


Chain A from PDB  Type:PROTEIN  Length:233
 aligned with WZZB_SHIFL | P37792 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:237
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       
           WZZB_SHIFL    55 KWTSTAIITQPDVGQIAGYNNAMNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPSVKNQQLPLTVSYVGQTAEGAQMKLAQYIQQVDDKVNQELEKDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIQEALQYANQAQVTKPQVQQTEDVTQDTLFLLGSEALESMIKHEATRPLVFSPNYYQTRQNLLDIEKLKFDDLDIHAYRYVMKPTLPIRRDS 291
               SCOP domains d4e29a_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...----.eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e29 A  55 KWTSTAIITQPDVGQIAGYNNAmNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPSVK----PLTVSYVGQTAEGAQmKLAQYIQQVDDKVNQELERDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIEEALRYADEAKITQPQIQQTQDVTQDTmFLLGSDALKSmIQNEATRPLAFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVmKPTLPVRRDS 291
                                    64        74  |     84        94       104       114       124 |    |134       144 |     154       164       174       184       194       204       214       224   |   234    |  244       254       264       274      |284       
                                                 77-MSE                                          126  131            146-MSE                                                                           228-MSE    239-MSE                                   281-MSE      


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with WZZB_SALTY | Q04866 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:235
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
           WZZB_SALTY    55 KWTSTAIITQPDAAQVATYTNALNVLYGGNAPKISEVQANFISRFSSAFSALSEVLDNQKEREKLTIEQSVKGQALPLSVSYVSTTAEGAQRRLAEYIQQVDEEVAKELEVDLKDNITLQTKTLQESLETQEVVAQEQKDLRIKQIEEALRYADEAKITQPQIQQTQDVTQDTMFLLGSDALKSMIQNEATRPLVFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVMKPTLPVRR 289
               SCOP domains d4e29b_ B: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhh.....eeeeee.-----..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e29 B  55 KWTSTAIITQPDVGQIAGYNNAmNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPS-----LPLTVSYVGQTAEGAQmKLAQYIQQVDDKVNQELERDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIEEALRYADEAKITQPQIQQTQDVTQDTmFLLGSDALKSmIQNEATRPLAFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVmKPTLPVRR 289
                                    64        74  |     84        94       104       114       124     | 134       144 |     154       164       174       184       194       204       214       224   |   234    |  244       254       264       274      |284     
                                                 77-MSE                                        124   130             146-MSE                                                                           228-MSE    239-MSE                                   281-MSE    


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with WZZB_SHIFL | P37792 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:235
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
           WZZB_SHIFL    55 KWTSTAIITQPDVGQIAGYNNAMNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPSVKNQQLPLTVSYVGQTAEGAQMKLAQYIQQVDDKVNQELEKDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIQEALQYANQAQVTKPQVQQTEDVTQDTLFLLGSEALESMIKHEATRPLVFSPNYYQTRQNLLDIEKLKFDDLDIHAYRYVMKPTLPIRR 289
               SCOP domains d4e29b_ B: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhh.....eeeeee.-----..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e29 B  55 KWTSTAIITQPDVGQIAGYNNAmNVIYGQAAPKVSDLQETLIGRFSSAFSALAETLDNQEEPEKLTIEPS-----LPLTVSYVGQTAEGAQmKLAQYIQQVDDKVNQELERDLKDNIALGRKNLQDSLRTQEVVAQEQKDLRIRQIEEALRYADEAKITQPQIQQTQDVTQDTmFLLGSDALKSmIQNEATRPLAFSPAYYQTKQTLLDIKNLKVTADTVHVYRYVmKPTLPVRR 289
                                    64        74  |     84        94       104       114       124     | 134       144 |     154       164       174       184       194       204       214       224   |   234    |  244       254       264       274      |284     
                                                 77-MSE                                        124   130             146-MSE                                                                           228-MSE    239-MSE                                   281-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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E29)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (WZZB_SALTY | Q04866)
biological process
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (WZZB_SHIFL | P37792)
biological process
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Databases and Analysis Tools

(-) Databases

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  4e29
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  WZZB_SALTY | Q04866
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  WZZB_SHIFL | P37792
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 Related Entries

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

UniProtKB/Swiss-Prot
        WZZB_SALTY | Q04866: 3b8p 4e2c
        WZZB_SHIFL | P37792: 4e2c 4e2h 4zm1 4zm5

(-) Related Entries Specified in the PDB File

3b80 WZZE POLYSACCHARRIDE CO-POLYMERASE
3b8m FEPE LPS O-ANTIGEN CHAIN LENGTH REGULATOR
3b8p SALMONELLA TYPHIMURIUM WZZB
4e2c
4e2h
4e2l