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(-) Description

Title :  X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.
 
Authors :  A. P. Kuzin, W. Edstrom, T. Skarina, Y. Korniyenko, A. Savchenko, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  13 Feb 04  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Unknown Function, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Blankenfeldt, A. P. Kuzin, T. Skarina, Y. Korniyenko, L. Tong, P. Bayer, P. Janning, L. S. Thomashow, D. V. Mavrodi
Structure And Function Of The Phenazine Biosynthetic Protein Phzf From Pseudomonas Fluorescens.
Proc. Natl. Acad. Sci. Usa V. 101 16431 2004
PubMed-ID: 15545603  |  Reference-DOI: 10.1073/PNAS.0407371101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YDDE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YDDE, B1464
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ORFB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:53 , ASP A:54 , ASP A:55 , THR A:97BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREPRO A:128 , GLN A:155 , HIS A:238 , HIS A:239BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWARETHR A:93 , TRP A:95 , ARG A:104BINDING SITE FOR RESIDUE SO4 A 603
4AC4SOFTWAREARG A:104 , PRO A:150 , LYS A:169BINDING SITE FOR RESIDUE SO4 A 604
5AC5SOFTWARECYS A:72 , GLY A:73 , HIS A:74 , THR A:225 , GLY A:226 , ASN A:227BINDING SITE FOR RESIDUE SO4 A 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SDJ)

(-) 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:310
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:310
                                       1                                                                                                                                                                                                                                                                                                     297  
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       | -
           YDDE_ECOLI     - -----------MKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL--   -
               SCOP domains d1sdja1 A:-10-129 Hypothetical protein YddE                                                                                                 d1sdja2 A:130-299 Hypothetical protein YddE                                                                                                                                SCOP domains
               CATH domains 1sdjA01 A:-10-121,A:285-299 Diaminopimelate Epimerase; Chain A, domain 1                                                            1sdjA02 A:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1sdjA01         CATH domains
               Pfam domains ------------------PhzC-PhzF-1sdjA01 A:8-291                                                                                                                                                                                                                                                                   -------- Pfam domains
         Sec.struct. author hhhhhhhhh.....eeeeeee........eeeeeee.....hhhhhhhhhhhhh...eeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeeeee..ee....hhhhhhhhhhhh..hhhhh......eeee....eeeee............hhhhhhhhhhhhh...eeeeee.....eeee.ee.......ee..hhhhhhhhhhhhhhh........eeeeeeee.......eeeeeeeeee..eeeeeeeee.eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sdj A -10 SGRENLYFQGHmKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQmQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVmIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRmFSPAIGIVEDPVTGNANGPmGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGmIEVTVTIRDNQPEKVTISGTAVILFHAEWAIELGS 299
                                    -1 |       9        19        29     |  39        49        59        69        79        89        99       109       119       129       139       149       159     | 169       179       189       199       209  |    219       229  |    239       249       259    |  269       279       289       299
                                       1-MSE                            35-MSE                                                                                                                           165-MSE                                        212-MSE             232-MSE                         264-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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    Phe A:25 - Pro A:26   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1p9v THIS IS RENUMBERED COORDINATES.
et25