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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI TWIN ARGININE LEADER PEPTIDE BINDING PROTEIN DMSD IN A MONOMERIC FORM
 
Authors :  C. M. Stevens, M. Paetzel
Date :  09 Sep 08  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Twin-Arginine Translocation (Tat), Protein Targeting, Protein Translocation, Chaperone, Leader Peptide, Signal Peptide, Redox Enzyme Maturation Protein (Remp) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Stevens, T. M. Winstone, R. J. Turner, M. Paetzel
Structural Analysis Of A Monomeric Form Of The Twin-Arginin Leader Peptide Binding Chaperone Escherichia Coli Dmsd.
J. Mol. Biol. V. 389 124 2009
PubMed-ID: 19361518  |  Reference-DOI: 10.1016/J.JMB.2009.03.069

(-) Compounds

Molecule 1 - TWIN-ARGININE LEADER-BINDING PROTEIN DMSD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET-A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DMSD, YNFI, B1591, JW5262
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 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  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:87 , ASN A:122 , GLU A:123 , TRS A:207 , GLU B:140 , HOH B:718 , HOH B:769BINDING SITE FOR RESIDUE TRS A 205
02AC2SOFTWAREARG A:161 , VAL A:165 , GLU A:168 , LYS A:169 , SER A:191 , ARG A:204 , HOH A:710 , HOH A:713 , HOH A:831BINDING SITE FOR RESIDUE GOL A 206
03AC3SOFTWARETYR A:22 , TRP A:72 , PHE A:76 , LYS A:120 , GLU A:123 , HIS A:127 , TRS A:205BINDING SITE FOR RESIDUE TRS A 207
04AC4SOFTWAREALA A:81 , LEU A:82 , PRO A:83 , LEU A:193 , LEU A:194 , ILE A:195 , PRO A:196 , GOL A:210 , HOH A:710 , HOH A:728 , HOH A:853BINDING SITE FOR RESIDUE GOL A 208
05AC5SOFTWAREPRO A:85 , HOH A:698 , HOH A:848 , HOH A:861 , HOH B:805BINDING SITE FOR RESIDUE GOL A 209
06AC6SOFTWAREALA A:81 , LEU A:82 , ARG A:204 , GOL A:208 , HOH A:812 , HOH A:852BINDING SITE FOR RESIDUE GOL A 210
07AC7SOFTWAREGLY A:100 , HOH A:872BINDING SITE FOR RESIDUE CL A 211
08AC8SOFTWARETHR A:145BINDING SITE FOR RESIDUE CL A 213
09AC9SOFTWAREPRO A:201 , LEU A:202 , HOH A:792 , GLN B:7 , ASP B:8 , GLN B:188 , GLN B:192 , HOH B:817BINDING SITE FOR RESIDUE GOL B 205
10BC1SOFTWARETRP B:153 , HOH B:793 , HOH B:851BINDING SITE FOR RESIDUE TRS B 206
11BC2SOFTWAREGLN B:6 , GLN B:7 , ASP B:8 , HOH B:841 , HOH B:872BINDING SITE FOR RESIDUE TRS B 207
12BC3SOFTWAREALA B:31 , VAL B:34 , ALA B:35 , THR B:38 , HIS B:68 , HOH B:856 , HOH B:864BINDING SITE FOR RESIDUE GOL B 208
13BC4SOFTWAREARG B:143 , HOH B:683 , HOH B:720BINDING SITE FOR RESIDUE CL B 209
14BC5SOFTWAREHOH A:869 , HOH B:735BINDING SITE FOR RESIDUE CL B 210
15BC6SOFTWAREGLN B:6 , ALA B:139 , HOH B:801 , HOH B:802 , HOH B:829BINDING SITE FOR RESIDUE CL B 211
16BC7SOFTWAREGLN B:144 , THR B:145 , GLU B:146BINDING SITE FOR RESIDUE NA B 212

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:78 -Pro A:79
2Gly B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EFP)

(-) 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:204
 aligned with DMSD_ECOLI | P69853 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           DMSD_ECOLI     1 MTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR 204
               SCOP domains d3efpa_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 3efpA00 A:1-204 TorD-like                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3efp A   1 MTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with DMSD_ECOLI | P69853 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:208
                                1                                                                                                                                                                                                           
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        
           DMSD_ECOLI     - ----MTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR 204
               SCOP domains d3efpb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 3efpB00 B:-3-204 TorD-like                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhhhh......hhhhhhhhh..hhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efp B  -3 RWGSMTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR 204
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DMSD_ECOLI | P69853)
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).
    GO:0005048    signal sequence binding    Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
biological process
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    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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 Related Entries

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        DMSD_ECOLI | P69853: 3cw0 3u41

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