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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN YPJQ FROM BACILLUS SUBTILIS, PFAM DUF64
 
Authors :  R. Kniewel, K. R. Rajashankar, V. Solorzano, C. D. Lima, S. K. Burley, Ne Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  09 Jun 04  (Deposition) - 22 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Ypjq, Bacillus Subtilis, Structural Genomics, Nysgxrc, T1519, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kniewel, K. R. Rajashankar, V. Solorzano, C. D. Lima
Crystal Structure Of A Hypothetical Protein From Bacillus Subtilis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YPJQ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETT7
    Expression System Strain: B834 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YPJQ, BSU21830
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:96 , ASP A:99 , GLU A:100 , HOH A:198 , HOH A:199 , HOH A:210BINDING SITE FOR RESIDUE CA A 190

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TLQ)

(-) 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:161
 aligned with YPJQ_BACSU | P54173 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:161
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163 
           YPJQ_BACSU     4 YTMNEMVDITKDMLNKRGVMIEDIARIVQKLQEKYNPNLPLSVCMENVEKVLNKREIIHAVLTGLALDQLAEQKLLPEPLQHLVETDEPLYGIDEIIPLSIVNVYGSIGLTNFGYLDKEKIGIIKELDESPDGIHTFLDDIVAALAAAAASRIAHTHQDLQ 164
               SCOP domains d1tlqa_ A: Hypothetical protein YpjQ                                                                                                                              SCOP domains
               CATH domains 1tlqA00 A:6-166 YutG-like                                                                                                                                         CATH domains
               Pfam domains ------PgpA-1tlqA01 A:12-160                                                                                                                                ------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlq A   6 YTmNEmVDITKDmLNKRGVmIEDIARIVQKLQEKYNPNLPLSVCmENVEKVLNKREIIHAVLTGLALDQLAEQKLLPEPLQHLVETDEPLYGIDEIIPLSIVNVYGSIGLTNFGYLDKEKIGIIKELDESPDGIHTFLDDIVAALAAAAASRIAHTHQDLQ 166
                              |  |  15  |     25        35        45    |   55        65        75        85        95       105       115       125       135       145       155       165 
                              |  |     18-MSE 25-MSE                   50-MSE                                                                                                                
                              8-MSE                                                                                                                                                          
                                11-MSE
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: PgpA] (3)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (YPJQ_BACSU | P54173)
molecular function
    GO:0008962    phosphatidylglycerophosphatase activity    Catalysis of the reaction: phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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