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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND PROPIONATE

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

Date :   11 Apr 07 (Deposition) - 29 May 07 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.44

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

Keywords :   Yjgf/Yer057C/Uk114 Family, 2-Ketobutyrate, Unknown Function, Propionate, Tdcf Protein, Ligand Binding (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	OCS	3	Mod. Amino Acid	CYSTEINESULFONIC ACID
2	PPI	2	Ligand/Ion	PROPANOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:84 , ARG B:105 , SER B:106 , CYS B:107 , GLY C:31 , GLU C:120	BINDING SITE FOR RESIDUE PPI B1129
2	AC2	SOFTWARE	PHE C:84 , ARG C:105 , SER C:106 , CYS C:107 , HOH C:2062	BINDING SITE FOR RESIDUE PPI C1129

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

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

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

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 2UYP)

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 d2uypa_ A: automated matches                                                                                                    SCOP domains
               CATH domains 2uypA00 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.hhhhhhhhhhhhhhhhhh......eeeeee...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyp A   2 KKIIETQRAPGAIGPYVQGVDLGSMVFTSGQIPVcPQTGEIPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQATYPTRSCVQVARLPKDVKLEIEAIAVRS 128
                                    11        21        31    |   41        51        61        71        81        91       101       111       121       
                                                             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 d2uypb_ B: automated matches                                                                                                     SCOP domains
               CATH domains 2uypB00 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.hhhhhhhhhhhhhhhhhh......eeeeee...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyp 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 d2uypc_ C: automated matches                                                                                                    SCOP domains
               CATH domains 2uypC00 C:2-128  [code=3.30.1330.40, no name defined]                                                                           CATH domains
           Pfam domains (1) -----Ribonuc_L-PSP-2uypC01 C:7-127                                                                                            - Pfam domains (1)
           Pfam domains (2) -----Ribonuc_L-PSP-2uypC02 C:7-127                                                                                            - Pfam domains (2)
           Pfam domains (3) -----Ribonuc_L-PSP-2uypC03 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
                 2uyp 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	d2uypa_	A:
1b	d2uypb_	B:
1c	d2uypc_	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	2uypA00	A:2-128
1b	2uypC00	C:2-128
1c	2uypB00	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-2uypC01	C:7-127
1b	Ribonuc_L-PSP-2uypC02	C:7-127
1c	Ribonuc_L-PSP-2uypC03	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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UniProtKB/Swiss-Prot
	TDCF_ECOLI \| P0AGL2	:	2uyj 2uyk 2uyn

2uyj	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND ETHYLENE GLYCOL
2uyk	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND SERINE
2uyn	CRYSTAL STRUCTURE OF E. COLI TDCF WITH BOUND 2-KETOBUTYRATE

Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

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