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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE
 
Authors :  A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Camb Y. Bourne
Date :  10 Sep 03  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Phenazine Biosynthesis Protein; Epimerase; Antibiotic Biosynthesis Protein; Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Cambillau, Y. Bourne
Crystal Structure Of E. Coli Ydde Protein Reveals A Strikin Homology With Diaminopimelate Epimerase
Proteins V. 55 764 2004
PubMed-ID: 15103639  |  Reference-DOI: 10.1002/PROT.20025

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YDDE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: TUNER(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YDDE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ORFB

 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 1QYA)

(-) Sites  (0, 0)

(no "Site" information available for 1QYA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:25 -Pro A:26
2Phe B:25 -Pro B:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QYA)

(-) 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:293
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
           YDDE_ECOLI     1 MKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains d1qyaa1 A:1-129 Hypothetical protein YddE                                                                                        d1qyaa2 A:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains 1qyaA01 A:1-121,A:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                   1qyaA02 A:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qyaA01       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeee.....hhhhhhhhhhhhh...eeeee......eeeeee....ee..--hhhhhhhhhhhhhhh...eeeeee..--.eeeeeeee..eeeeeee....ee.....hhhhhhhhhhh..hhhhh......eeee....eeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.hhhh..eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qya A   1 LKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPI--HATVAAHYVRAKVLGLGNCTIWQTSL--KHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                                    10        20        30        40        50        60        70|  |    80        90        |- |     110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
                                                                                                 71 74                       99  |                                                                                                                                                                                                   
                                                                                                                               102                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:307
                                      1                                                                                                                                                                                                                                                                                                        
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
           YDDE_ECOLI     - ----------MKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains ----------d1qyab1 B:1-129 Hypothetical protein YddE                                                                                        d1qyab2 B:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains 1qyaB01 B:-9-121,B:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                            1qyaB02 B:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qyaB01       CATH domains
           Pfam domains (1) -----------------PhzC-PhzF-1qyaB01 B:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (1)
           Pfam domains (2) -----------------PhzC-PhzF-1qyaB02 B:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (2)
         Sec.struct. author ...hhhhhhh...eeeeeee........eeeeeee.....hhhhhhhhhhhhh...eeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee....ee....hhhhhhhhhhhh..hhhhh......eeee....eeeeee....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.......eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qya B  -9 ESTSLYKKAGLKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DAP_epimerase (14)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YDDE_ECOLI | P37757)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  Sites
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  Cis Peptide Bonds
    Phe A:25 - Pro A:26   [ RasMol ]  
    Phe B:25 - Pro B:26   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        YDDE_ECOLI | P37757: 1qy9 1sdj

(-) Related Entries Specified in the PDB File

1qy9