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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND ETHYLENE GLYCOL

Authors :   J. D. Burman, C. E. M. Stevenson, R. G. Sawers, D. M. Lawson

Date :   10 Apr 07 (Deposition) - 29 May 07 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Yjgf/Yer057C/Uk114 Family, Ethylene Glycol, Unknown Function, 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

Molecule 1 - PROTEIN TDCF
	Chains	:	A, 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

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	OCS	3	Mod. Amino Acid	CYSTEINESULFONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:105 , CYS B:107 , GLY C:31 , GLU C:120	BINDING SITE FOR RESIDUE EDO B1129
2	AC2	SOFTWARE	GLY A:31 , ARG C:105 , CYS C:107	BINDING SITE FOR RESIDUE EDO C1129

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

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

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

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0076	PS01094	Uncharacterized protein family UPF0076 signature.	TDCF_ECOLI	103-121	3	A:103-121 B:103-121 C:103-121

(no "Exon" information available for 2UYJ)

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:128
 aligned with TDCF_ECOLI | P0AGL2 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           TDCF_ECOLI     1 MKKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
               SCOP domains d2uyja_ A: automated matches                                                                                                     SCOP domains
               CATH domains 2uyjA00 A:1-128  [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
                 2uyj A   1 MKKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    10        20        30     |  40        50        60        70        80        90       100       110       120        
                                                              36-OCS

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with TDCF_ECOLI | P0AGL2 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           TDCF_ECOLI     1 MKKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVCPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
               SCOP domains d2uyjb_ B: automated matches                                                                                                     SCOP domains
               CATH domains 2uyjB00 B:1-128  [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
                 2uyj B   1 MKKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    10        20        30     |  40        50        60        70        80        90       100       110       120        
                                                              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 d2uyjc_ C: automated matches                                                                                                    SCOP domains
               CATH domains 2uyjC00 C:2-128  [code=3.30.1330.40, no name defined]                                                                           CATH domains
           Pfam domains (1) -----Ribonuc_L-PSP-2uyjC01 C:7-127                                                                                            - Pfam domains (1)
           Pfam domains (2) -----Ribonuc_L-PSP-2uyjC02 C:7-127                                                                                            - Pfam domains (2)
           Pfam domains (3) -----Ribonuc_L-PSP-2uyjC03 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
                 2uyj 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Bacillus chorismate mutase-like (324)

Superfamily: YjgF-like (45)

Family: YjgF/L-PSP (23)

Protein domain: automated matches (8)

Escherichia coli [TaxId: 562] (4)

1a	d2uyja_	A:
1b	d2uyjb_	B:
1c	d2uyjc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.40, no name defined] (35)

Escherichia coli. Organism_taxid: 562. Strain: mc4100. (4)

1a	2uyjC00	C:2-128
1b	2uyjA00	A:1-128
1c	2uyjB00	B:1-128

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribonuc_L-PSP] (16)

Family: Ribonuc_L-PSP (16)

Escherichia coli (strain K12) (5)

1a	Ribonuc_L-PSP-2uyjC01	C:7-127
1b	Ribonuc_L-PSP-2uyjC02	C:7-127
1c	Ribonuc_L-PSP-2uyjC03	C:7-127

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.

Asymmetric/Biological Unit
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	TDCF_ECOLI \| P0AGL2	:	2uyk 2uyn 2uyp

2uyk	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND SERINE
2uyn	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND 2-KETOBUTYRATE
2uyp	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND PROPIONATE

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

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