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(-) Description

Title :  CRYSTAL STRUCTURE OF YGFY FROM ESCHERICHIA COLI
 
Authors :  K. Lim, V. Doseeva, E. Sarikaya Demirkan, S. Pullalarevu, W. Krajewski, A. Galkin, A. Howard, O. Herzberg, Structure 2 Function Project (S2F)
Date :  11 Aug 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Ygfy, Hypothetical Protein, Transcriptional Regulation, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lim, V. Doseeva, E. Sarikaya Demirkan, S. Pullalarevu, W. Krajewski, A. Galkin, A. Howard, O. Herzberg
Crystal Structure Of The Ygfy From Escherichia Coli, A Protein That May Be Involved In Transcriptional Regulation
Proteins V. 58 759 2005
PubMed-ID: 15593094  |  Reference-DOI: 10.1002/PROT.20337
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YGFY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET100/D-TOPO
    Gene: YGFY
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X6I)

(-) Sites  (0, 0)

(no "Site" information available for 1X6I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X6I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X6I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X6I)

(-) Exons   (0, 0)

(no "Exon" information available for 1X6I)

(-) 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:89
 aligned with SDHE_ECOLI | P64559 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:89
                             1                                                                                       
                             |       9        19        29        39        49        59        69        79         
           SDHE_ECOLI     - -MDINNKARIHWACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRERGPVAI  88
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x6iA00 A:0-88 Ygfy                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1x6i A   0 HMDINNKARIHWACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRERGPVAI  88
                                     9        19        29        39        49        59        69        79         


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with SDHE_ECOLI | P64559 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
           SDHE_ECOLI     1 MDINNKARIHWACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRERGPVA  87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x6iB00 B:201-287 Ygfy                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhh.ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1x6i B 201 MDINNKARIHWACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRERGPVA 287
                                   210       220       230       240       250       260       270       280
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 1X6I)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X6I)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SDHE_ECOLI | P64559)
biological process
    GO:0017013    protein flavinylation    The addition of a flavin group to a protein amino acid.
    GO:0006105    succinate metabolic process    The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SDHE_ECOLI | P64559: 1x6j

(-) Related Entries Specified in the PDB File

ygfy
1x6j