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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND 2-KETOBUTYRATE
 
Authors :  J. D. Burman, C. E. M. Stevenson, R. G. Sawers, D. M. Lawson
Date :  11 Apr 07  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Unknown Function, Yjgf/Yer057C/Uk114 Family, Tdcf Protein, Ligand Binding, 2-Ketobutyrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Burman, C. E. M. Stevenson, R. G. Sawers, D. M. Lawson
The Crystal Structure Of Escherichia Coli Tdcf, A Member Of The Highly Conserved Yjgf/Yer057C/Uk114 Family.
Bmc Struct. Biol. V. 7 30 2007
PubMed-ID: 17506874  |  Reference-DOI: 10.1186/1472-6807-7-30

(-) Compounds

Molecule 1 - PROTEIN TDCF
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETHF1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC4100
    Synonym: TDCF
 
Molecule 2 - PROTEIN TDCF
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETHF1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC4100
    Synonym: TDCF

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
12KT3Ligand/Ion2-KETOBUTYRIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3OCS3Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:84 , ARG A:105 , SER A:106 , CYS A:107 , HOH A:2101 , TYR B:17 , GLY B:31 , ILE B:33 , GLU B:120BINDING SITE FOR RESIDUE 2KT A1129
2AC2SOFTWAREPHE B:84 , ARG B:105 , SER B:106 , CYS B:107 , HOH B:2127 , TYR C:17 , GLY C:31 , ILE C:33 , GLU C:120BINDING SITE FOR RESIDUE 2KT B1129
3AC3SOFTWAREGLY A:31 , ILE A:33 , GLU A:120 , PHE C:84 , ARG C:105 , SER C:106 , CYS C:107 , HOH C:2138 , HOH C:2139BINDING SITE FOR RESIDUE 2KT C1129

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2UYN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0076PS01094 Uncharacterized protein family UPF0076 signature.TDCF_ECOLI103-121
 
 		  3A:103-121
B:103-121
C:103-121

(-) Exons   (0, 0)

(no "Exon" information available for 2UYN)

(-) 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:127
 aligned with TDCF_ECOLI | P0AGL2 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           TDCF_ECOLI     2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
               SCOP domains d2uyna_ A: automated matches                                                                                                    SCOP domains
               CATH domains 2uynA00 A:2-128  [code=3.30.1330.40, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..............eee...eeee...............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyn A   2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVkAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    11        21        31    |   41        51      | 61        71        81        91       101       111       121       
                                                             36-OCS                58-KCX                                                                  


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with TDCF_ECOLI | P0AGL2 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           TDCF_ECOLI     2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
               SCOP domains d2uynb_ B: automated matches                                                                                                    SCOP domains
               CATH domains 2uynB00 B:2-128  [code=3.30.1330.40, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..............eee...eeee...............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyn B   2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    11        21        31    |   41        51        61        71        81        91       101       111       121       
                                                             36-OCS                                                                                        


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with TDCF_ECOLI | P0AGL2 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           TDCF_ECOLI     2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
               SCOP domains d2uync_ C: automated matches                                                                                                    SCOP domains
               CATH domains 2uynC00 C:2-128  [code=3.30.1330.40, no name defined]                                                                           CATH domains
           Pfam domains (1) -----Ribonuc_L-PSP-2uynC01 C:7-127                                                                                            - Pfam domains (1)
           Pfam domains (2) -----Ribonuc_L-PSP-2uynC02 C:7-127                                                                                            - Pfam domains (2)
           Pfam domains (3) -----Ribonuc_L-PSP-2uynC03 C:7-127                                                                                            - Pfam domains (3)
         Sec.struct. author .eee..............eee...eeee...............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyn C   2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    11        21        31    |   41        51        61        71        81        91       101       111       121       
                                                             36-OCS
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribonuc_L-PSP] (16)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (TDCF_ECOLI | P0AGL2)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
biological process
    GO:0070689    L-threonine catabolic process to propionate    The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form the compound propionate.
    GO:0006566    threonine metabolic process    The chemical reactions and pathways involving threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDCF_ECOLI | P0AGL2: 2uyj 2uyk 2uyp

(-) Related Entries Specified in the PDB File

2uyj CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND ETHYLENE GLYCOL
2uyk CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND SERINE
2uyp CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND PROPIONATE