1TF1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE E. COLI GLYOXYLATE REGULATORY PROTEIN LIGAND BINDING DOMAIN

Authors :   J. R. Walker, T. Skarina, M. Kudrytska, A. Joachimiak, C. Arrowsmith, A. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   26 May 04 (Deposition) - 03 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Midwest Center For Structural Genomics, Glcr, Ligand Binding Domain, Transcriptional Regulator, Psi, Protein Structure Initiative, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, S. Altamentova, A. Ezersky, G. Lorca, T. Skarina, M. Kudritska, L. J. Ball, A. Bochkarev, A. Savchenko
Structural And Biochemical Study Of Effector Molecule Recognition By The E. Coli Glyoxylate And Allantoin Utilization Regulatory Protein Allr.
J. Mol. Biol. V. 358 810 2006
PubMed-ID: 16546208 | Reference-DOI: 10.1016/J.JMB.2006.02.034
(for further references see the PDB file header)

Molecule 1 - NEGATIVE REGULATOR OF ALLANTOIN AND GLYOXYLATE UTILIZATION OPERONS
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	GLXA3
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRANSCRIPTIONAL REGULATOR ALLR, APC5051

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1TF1)

(no "Site" information available for 1TF1)

(no "SS Bond" information available for 1TF1)

(no "Cis Peptide Bond" information available for 1TF1)

(no "SAP(SNP)/Variant" information available for 1TF1)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ICLR	PS51077	IclR-type HTH domain profile.	ALLR_ECOLI	21-83	2	A:8-10 D:8-10
2	ICLR_ED	PS51078	IclR effector binding domain profile.	ALLR_ECOLI	84-267	4	A:12-182 B:12-182 C:12-182 D:12-182

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ICLR	PS51077	IclR-type HTH domain profile.	ALLR_ECOLI	21-83	1	A:8-10 -
2	ICLR_ED	PS51078	IclR effector binding domain profile.	ALLR_ECOLI	84-267	1	A:12-182 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ICLR	PS51077	IclR-type HTH domain profile.	ALLR_ECOLI	21-83	0	- -
2	ICLR_ED	PS51078	IclR effector binding domain profile.	ALLR_ECOLI	84-267	1	- B:12-182 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ICLR	PS51077	IclR-type HTH domain profile.	ALLR_ECOLI	21-83	0	- -
2	ICLR_ED	PS51078	IclR effector binding domain profile.	ALLR_ECOLI	84-267	1	- - C:12-182 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ICLR	PS51077	IclR-type HTH domain profile.	ALLR_ECOLI	21-83	1	- D:8-10
2	ICLR_ED	PS51078	IclR effector binding domain profile.	ALLR_ECOLI	84-267	1	- - - D:12-182

(no "Exon" information available for 1TF1)

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:184
 aligned with ALLR_ECOLI | P0ACN4 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:262
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  
           ALLR_ECOLI     8 GRPGQAEPVAQKGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLKA 269
               SCOP domains d1                                                         tf1a_ A      :                Transcriptional regulator AllR, C-terminal domain                                                                                                                             SCOP domains
               CATH domains 1t                                                         f1A00 A      :1               -184  [code=3.30.450.40, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------------------------------------------------....hhh------hh---------------hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeee.....eee......eee...hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------HTH_ICLR  PDB: A:8-10 UniProt: 21-83                           ICLR_ED  PDB: A:12-182 UniProt: 84-267                                                                                                                                                  -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf1 A   1 GR---------------------------------------------------------ENLYFQG------HM---------------DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLKA 184
                             |       -         -         -         -         -         3     |   -  ||     -        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  
                             2                                                         3     9     10|              12                                                                                                                                                                            
                                                                                                    11

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with ALLR_ECOLI | P0ACN4 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:199
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         
           ALLR_ECOLI    70 VYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 268
               SCOP domains d1tf      1b               _ B: Transcriptional regulator AllR, C-terminal domain                                                                                                                       SCOP domains
               CATH domains 1tf1      B0               0 B:6-183  [code=3.30.450.40, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh------hh---------------hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_ICLR      ICLR_ED  PDB: B:12-182 UniProt: 84-267                                                                                                                                                  - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf1 B   6 YFQG------HM---------------DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 183
                               |     -||       -       |14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174         
                               9     10|              12                                                                                                                                                                           
                                      11

Chain C from PDB  Type:PROTEIN  Length:179
 aligned with ALLR_ECOLI | P0ACN4 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:200
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
           ALLR_ECOLI    69 FVYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 268
               SCOP domains d1tf1      c_                C: Transcriptional regulator AllR, C-terminal domain                                                                                                                        SCOP domains
               CATH domains 1tf1C      00                C:5-183  [code=3.30.450.40, no name defined]                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh------hh---------------hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeee..............eee...hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_ICLR  PDB: ICLR_ED  PDB: C:12-182 UniProt: 84-267                                                                                                                                                  - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf1 C   5 LYFQG------HM---------------DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 183
                                |    - ||      -        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
                                9     10|              12                                                                                                                                                                           
                                       11

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with ALLR_ECOLI | P0ACN4 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:261
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267 
           ALLR_ECOLI     8 GRPGQAEPVAQKGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 268
               SCOP domains d1                                                         tf1d_ D      :                Transcriptional regulator AllR, C-terminal domain                                                                                                                            SCOP domains
               CATH domains 1t                                                         f1D00 D      :1               -183  [code=3.30.450.40, no name defined]                                                                                                                                    CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------IclR-1tf1D01 D:54-179                                                                                                         ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------IclR-1tf1D02 D:54-179                                                                                                         ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------IclR-1tf1D03 D:54-179                                                                                                         ---- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------IclR-1tf1D04 D:54-179                                                                                                         ---- Pfam domains (4)
         Sec.struct. author ..---------------------------------------------------------....hhh------hh---------------hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeee..............ee....hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------HTH_ICLR  PDB: D:8-10 UniProt: 21-83                           ICLR_ED  PDB: D:12-182 UniProt: 84-267                                                                                                                                                  - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf1 D   1 GR---------------------------------------------------------ENLYFQG------HM---------------DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLK 183
                             |       -         -         -         -         -         3     |   -  ||     -        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
                             2                                                         3     9     10|              12                                                                                                                                                                           
                                                                                                    11

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: IclR ligand-binding domain-like (5)

Protein domain: Transcriptional regulator AllR, C-terminal domain (1)

Escherichia coli [TaxId: 562] (1)

1a	d1tf1a_	A:
1b	d1tf1b_	B:
1c	d1tf1c_	C:
1d	d1tf1d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: [code=3.30.450.40, no name defined] (27)

Escherichia coli. Organism_taxid: 562. (5)

1a	1tf1B00	B:6-183
1b	1tf1C00	C:5-183
1c	1tf1D00	D:1-183
1d	1tf1A00	A:1-184

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: IclR (7)

Escherichia coli (strain K12) (5)

1a	IclR-1tf1D01	D:54-179
1b	IclR-1tf1D02	D:54-179
1c	IclR-1tf1D03	D:54-179
1d	IclR-1tf1D04	D:54-179

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ALLR_ECOLI | P0ACN4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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1mkm	CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA 0065, A MEMBER OF THE ICLR TRANSCRIPTIONAL FACTOR FAMILY RELATED ID: APC5051 RELATED DB: TARGETDB
1t9l	CRYSTAL STRUCTURE OF THE E. COLI GLYOXYLATE REGULATORY PROTEIN LIGAND BINDING DOMAIN COMPLEXED WITH GLYOXYLATE
1td5	CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF E. COLI ICLR

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