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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN YEDK FROM ESCHERICHIA COLI
 
Authors :  L. Chen, Z. J. Liu, Y. Li, M. Zhao, J. Rose, A. Ebihara, S. Yokoyama, B. C. W Southeast Collaboratory For Structural Genomics (Secsg), Rik Structural Genomics Initiative, Riken Structural Genomics/Pr Initiative (Rsgi)
Date :  13 Sep 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hypothetical Protein Yedk, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Riken, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, Z. J. Liu, Y. Li, M. Zhao, J. Rose, A. Ebihara, S. Yokoyama, B. C. Wang
Crystal Structure Of Hypothetical Protein Yedk From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YEDK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCR2.1-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YEDK
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ICU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ICU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:141 -Pro A:142
2Thr B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ICU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ICU)

(-) Exons   (0, 0)

(no "Exon" information available for 2ICU)

(-) 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:210
 aligned with YEDK_ECOLI | P76318 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           YEDK_ECOLI     3 GRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPV 222
               SCOP domains d2icua_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 2icuA00 A:10-229 hypothetical protein yedk domain like                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhh...hhhhh..........eeee....eeeeeeee..eeeeeeee......----....eeehhhhh....hhhhhhhheeeeee.eeee..------..eeeee.....eeeeeee..hhhhh.....eeeeeee.hhhhhhh..eee.eehhhhhhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2icu A  10 GRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPG----PPLINARVETAATSRmFKPLWQHGRAICFADGWFEWK------QPFFIYRADGQPIFmAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWmRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPV 229
                                    19        29        39        49        59        69   |    79        89   |    99       109    |    - |     129     | 139       149       159       169       179   |   189       199       209       219       229
                                                                                          73   78             93-MSE              114    121           135-MSE                                         183-MSE                                          


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with YEDK_ECOLI | P76318 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           YEDK_ECOLI     3 GRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPV 222
               SCOP domains d2icub_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 2icuB00 B:10-229 hypothetical protein yedk domain like                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhh...hhhhh..........eeee....eeeeeeee..eeeeeeee.......-......eeehhhhh....hhhhhhhheeeeee.eeee..------..eeeee.....eeeeeee..hhhhh.....eeeeeee.hhhhhhh..eee.eehhhhhhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2icu B  10 GRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERDEHLHLDPVFWGYAPGW-DKPPLINARVETAATSRmFKPLWQHGRAICFADGWFEWK------QPFFIYRADGQPIFmAAIGSTPFERGDEAEGFLIVTAAADQGLVDIHDRRPLVLSPEAAREWmRQEISGKEASEIAASGCVPANQFSWHPVSRAVGNVKNQGAELIQPV 229
                                    19        29        39        49        59        69    | | 79        89   |    99       109    |    - |     129     | 139       149       159       169       179   |   189       199       209       219       229
                                                                                           74 |               93-MSE              114    121           135-MSE                                         183-MSE                                          
                                                                                             76
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ICU)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YEDK_ECOLI | P76318)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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