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(-) Description

Title :  ATOMIC STRUCTURE OF A PUTATIVE ANAEROBIC DEHYDROGENASE COMPONENT
 
Authors :  Y. Qiu, R. Zhang, V. Tereshko, Y. Kim, F. Collart, A. Joachimiak, A. Koss Midwest Center For Structural Genomics (Mcsg)
Date :  05 Feb 04  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Anaerobic Dehydrogenases Component, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Qiu, R. Zhang, T. A. Binkowski, V. Tereshko, A. Joachimiak, A. Kossiakoff
The 1. 38 A Crystal Structure Of Dmsd Protein From Salmonell Typhimurium, A Proofreading Chaperone On The Tat Pathway.
Proteins V. 71 525 2008
PubMed-ID: 18175314  |  Reference-DOI: 10.1002/PROT.21828

(-) Compounds

Molecule 1 - PUTATIVE COMPONENT OF ANAEROBIC DEHYDROGENASES
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
3SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:-1 , SER A:-2 , ASP A:41 , HOH A:627 , HOH A:677 , SO4 A:1000BINDING SITE FOR RESIDUE SO4 A 999
2AC2SOFTWAREASP A:41 , SO4 A:999BINDING SITE FOR RESIDUE SO4 A 1000
3AC3SOFTWAREILE A:77 , PRO A:79 , ALA A:81 , HOH A:843BINDING SITE FOR RESIDUE PEG A 303
4AC4SOFTWAREHIS A:144 , CYS A:147 , GLU A:148 , TRP A:189 , HOH A:659 , HOH A:742BINDING SITE FOR RESIDUE PEG A 304
5AC5SOFTWARELEU A:134 , HOH A:879 , HOH A:907BINDING SITE FOR RESIDUE PEG A 305
6AC6SOFTWAREHOH A:546 , HOH A:626 , HOH A:684 , HOH A:701 , HOH A:817BINDING SITE FOR RESIDUE PEG A 306
7AC7SOFTWAREGLU A:29 , LEU A:33 , HOH A:605 , HOH A:773BINDING SITE FOR RESIDUE PEG A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S9U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S9U)

(-) Exons   (0, 0)

(no "Exon" information available for 1S9U)

(-) Sequences/Alignments

Asymmetric/Biological 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:201
 aligned with DMSD_SALTY | Q8ZPK0 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:207
                               1                                                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       
           DMSD_SALTY     - ---MTTFLQRDDFAVTARVLGALFYYSPESHETAPLVQALLNDDWQAQWPLDAEALAPVAAMFKTHSEESLPQAWQRLFIGPYALPSPPWGSVWLDRESVLFGDSTLALRQWMRENGIQFEMQQNEPEDHFGSLLLLAAWLAENDRHHECEQLLAWHLFPWSSRFLDVFIDHAGHPFYQALGQLARLTLAQWQAQLIIPVAVKPLFR 204
               SCOP domains d1s9ua_ A: Putative component of anaerobic dehydrogenases YnfI                                                                                                                                                  SCOP domains
               CATH domains 1s9uA00 A:-2-204 TorD-like                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------Nitrate_red_del-1s9uA01 A:31-166                                                                                                        -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhh......hhhhhhhhhhhhhh...------....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9u A  -2 SDAmTTFLQRDEFAVTARVLGALFYYSPESHETAPLVQALLNDDWQAQWPLDAEALAPVAAmFKTHSEESLPQAWQRLFIGPYALPSPPWGSVWLDRESVLFGDSTLALRQWmRENGIQ------EPEDHFGSLLLLAAWLAENDRHHECEQLLAWHLFPWSSRFLDVFIDHAGHPFYQALGQLARLTLAQWQAQLIIPVAVKPLFR 204
                               |     7        17        27        37        47        57 |      67        77        87        97       107  |     |-     | 127       137       147       157       167       177       187       197       
                               |                                                        59-MSE                                            110-MSE16    123                                                                                 
                               1-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Nitrate_red_del] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DMSD_SALTY | Q8ZPK0)
molecular function
    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.

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  1s9u
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 Related Entries

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