2O99 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF E.COLI ICLR C-TERMINAL FRAGMENT IN COMPLEX WITH GLYOXYLATE

Authors :   V. V. Lunin, A. Ezersky, E. Evdokimova, M. Kudritska, A. Savchenko

Date :   13 Dec 06 (Deposition) - 10 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Iclr, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. L. Lorca, A. Ezersky, V. V. Lunin, J. R. Walker, S. Altamentova, E. Evdokimova, M. Vedadi, A. Bochkarev, A. Savchenko
Glyoxylate And Pyruvate Are Antagonistic Effectors Of The Escherichia Coli Iclr Transcriptional Regulator.
J. Biol. Chem. V. 282 16476 2007
PubMed-ID: 17426033 | Reference-DOI: 10.1074/JBC.M610838200
(for further references see the PDB file header)

Molecule 1 - ACETATE OPERON REPRESSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 40)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GOA	4	Ligand/Ion	GLYCOLIC ACID
3	MSE	32	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 20)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOA	2	Ligand/Ion	GLYCOLIC ACID
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 20)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOA	2	Ligand/Ion	GLYCOLIC ACID
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:70 , GLN A:74 , THR A:110 , GLY A:114 , ALA A:131 , CYS A:132 , HOH A:1042 , HOH A:1056	BINDING SITE FOR RESIDUE EDO A 801
2	AC2	SOFTWARE	GLN B:74 , THR B:110 , ARG B:111 , GLY B:114 , ALA B:131 , CYS B:132 , HOH B:947	BINDING SITE FOR RESIDUE EDO B 802
3	AC3	SOFTWARE	ALA C:70 , GLN C:74 , THR C:110 , GLY C:114 , CYS C:132 , HOH C:973	BINDING SITE FOR RESIDUE EDO C 803
4	AC4	SOFTWARE	GLN D:74 , THR D:110 , GLY D:114 , ALA D:131 , CYS D:132 , HOH D:1001 , HOH D:1010	BINDING SITE FOR RESIDUE EDO D 804
5	AC5	SOFTWARE	SER D:65 , GLY D:66 , ALA D:67 , ASP D:118 , CYS D:128 , SER D:145 , SER D:147	BINDING SITE FOR RESIDUE GOA D 901
6	AC6	SOFTWARE	SER A:65 , GLY A:66 , ALA A:67 , ASP A:118 , CYS A:128 , SER A:145 , SER A:147	BINDING SITE FOR RESIDUE GOA A 902
7	AC7	SOFTWARE	SER B:65 , GLY B:66 , ALA B:67 , ASP B:118 , CYS B:128 , SER B:145 , SER B:147	BINDING SITE FOR RESIDUE GOA B 903
8	AC8	SOFTWARE	SER C:65 , GLY C:66 , ALA C:67 , ASP C:118 , CYS C:128 , SER C:145 , SER C:147	BINDING SITE FOR RESIDUE GOA C 904

(no "SS Bond" information available for 2O99)

(no "Cis Peptide Bond" information available for 2O99)

(no "SAP(SNP)/Variant" information available for 2O99)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	3	A:4-178 B:4-178 C:4-178

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	1	A:4-178 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICLR_ED	PS51078	IclR effector binding domain profile.	ICLR_ECOLI	87-272	2	- B:4-178 C:4-178

(no "Exon" information available for 2O99)

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:178
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:197
                                                                                                                                                                                                                            274   
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    |  
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGMR--   -
               SCOP domains d2               o99a_ A: Transcriptional regulator IclR, C-terminal domain                                                                                                                           SCOP domains
               CATH domains 2o               99A00 A:1-182  [code=3.30.450.40, no name defined]                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......ee....hhhhhhhhh..hhhhhhh----............hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: A:4-178 UniProt: 87-272                                                                                                                                                     ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o99 A   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTK----KGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGmRGS 182
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75      |  - |      95       105       115       125       135       145       155       165       175   |   
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE              82   87                                                                          164-MSE        179-MSE
                                                                                             52-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:194
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGM 273
               SCOP domains d2               o99b_ B: Transcriptional regulator IclR, C-terminal domain                                                                                                                        SCOP domains
               CATH domains 2o               99B00 B:1-178  [code=3.30.450.40, no name defined]                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: B:4-178 UniProt: 87-272                                                                                                                                                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o99 B   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGm 179
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75        85        95       105       115       125       135       145       155       165       175   |
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                                                                                             52-MSE

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:197
                                                                                                                                                                                                                            274   
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    |  
           ICLR_ECOLI    80 GHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGMR--   -
               SCOP domains d2               o99c_ C: Transcriptional regulator IclR, C-terminal domain                                                                                                                           SCOP domains
               CATH domains 2o               99C00 C:1-182  [code=3.30.450.40, no name defined]                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee.....eee......eee...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ICLR_ED  PDB: C:4-178 UniProt: 87-272                                                                                                                                                     ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o99 C   1 GH---------------mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGmRGS 182
                             |       -       | 5        15   |    25  |     35        45    | | 55      | 65        75        85        95       105       115       125       135       145       155       165       175   |   
                             2               3-MSE          19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                                                                                             52-MSE

Chain D from PDB  Type:PROTEIN  Length:178
 aligned with ICLR_ECOLI | P16528 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:178
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        
           ICLR_ECOLI    97 QSRNLLAIVHPILRNLMEESGETVNMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVTLAYGGMR 274
               SCOP domains d2o99d_ D: Transcriptional regulator IclR, C-terminal domain                                                                                                                       SCOP domains
               CATH domains -2o99D00 D:4-180  [code=3.30.450.40, no name defined]                                                                                                                              CATH domains
           Pfam domains (1) ----------------------------------------------IclR-2o99D01 D:49-175                                                                                                          ----- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------IclR-2o99D02 D:49-175                                                                                                          ----- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------IclR-2o99D03 D:49-175                                                                                                          ----- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------IclR-2o99D04 D:49-175                                                                                                          ----- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.eeeeeee......eeeeeee.....eee......ee....hhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.eeee......eeeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ICLR_ED  PDB: - UniProt: 87-272                                                                                                                                                 -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o99 D   3 mSRNLLAIVHPILRNLmEESGETVNmAVLDQSDHEAIIIDQVQCTHLmRmSAPIGGKLPmHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAmVIKAAKEVTLAYGGmR 180
                            |       12      | 22     |  32        42       |52        62        72        82        92       102       112       122       132       142       152       162 |     172      | 
                            |              19-MSE   28-MSE                50-MSE      62-MSE                                                                                               164-MSE        179-MSE
                            3-MSE                                           52-MSE

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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 IclR, C-terminal domain (4)

Escherichia coli [TaxId: 562] (3)

1a	d2o99a_	A:
1b	d2o99b_	B:
1c	d2o99c_	C:
1d	d2o99d_	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. (2)

1a	2o99A00	A:1-182
1b	2o99D00	D:4-180
1c	2o99B00	B:1-178
1d	2o99C00	C:1-182

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: IclR (7)

Escherichia coli (strain K12) (5)

1a	IclR-2o99D01	D:49-175
1b	IclR-2o99D02	D:49-175
1c	IclR-2o99D03	D:49-175
1d	IclR-2o99D04	D:49-175

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ICLR_ECOLI | P16528)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	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.

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	2o99
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	ICLR_ECOLI \| P16528	:	1td5 2o9a

Description

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Ligands, Modified Residues, Ions (3, 40)

Sites (8, 8)

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