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Title :   CRYSTAL STRUCTURE OF PUTATIVE TRANSCRIPTIONAL REGULATOR YCDC

Authors :   Y. V. Patskovsky, A. A. Knapik, V. Mennella, S. K. Burley, W. Minor, S. C. York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   03 Feb 10 (Deposition) - 16 Mar 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Helix-Turn-Helix, Putative Transcriptional Regulator, Dimer, Uracil, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. V. Patskovsky, V. Mennella, S. C. Almo
Crystal Structure Of Hypothetical Transcriptional Regulator Ycdc From Escherichia Coli
To Be Published
PubMed: search

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	T7 TOPO-CT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1013, JW0998, RUTR, YCDC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	RUT OPERON REPRESSOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 20)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	URA	4	Ligand/Ion	URACIL

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	URA	2	Ligand/Ion	URACIL

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	URA	2	Ligand/Ion	URACIL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:76 , LYS A:100 , PHE A:114 , TRP A:166 , GLN A:170 , GLN B:178	BINDING SITE FOR RESIDUE URA A 212
2	AC2	SOFTWARE	PHE A:175 , GLN A:178 , LEU B:73 , TRP B:76 , LYS B:100 , TRP B:166 , GLN B:170 , HOH B:224	BINDING SITE FOR RESIDUE URA B 212
3	AC3	SOFTWARE	LEU C:73 , TRP C:76 , LYS C:100 , PHE C:114 , TRP C:166 , GLN C:170 , GLN D:178	BINDING SITE FOR RESIDUE URA C 212
4	AC4	SOFTWARE	PHE C:175 , GLN C:178 , LEU D:73 , TRP D:76 , LYS D:100 , PHE D:114 , TRP D:166 , GLN D:170	BINDING SITE FOR RESIDUE URA D 212

(no "SS Bond" information available for 3LOC)

(no "Cis Peptide Bond" information available for 3LOC)

(no "SAP(SNP)/Variant" information available for 3LOC)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	RUTR_ECOLI	17-77	4	A:16-76 B:16-76 C:16-76 D:16-76

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	RUTR_ECOLI	17-77	2	A:16-76 B:16-76 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	RUTR_ECOLI	17-77	2	- - C:16-76 D:16-76

(no "Exon" information available for 3LOC)

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:201
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3loca1 A:11-85 Hypothetical transcriptional regulator YcdC                d3loca2 A:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: A:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc A  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locb1 B:11-85 Hypothetical transcriptional regulator YcdC                d3locb2 B:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: B:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc B  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE

Chain C from PDB  Type:PROTEIN  Length:200
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:200
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
           RUTR_ECOLI    13 SRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locc1 C:12-85 Hypothetical transcriptional regulator YcdC               d3locc2 C:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_TETR_2  PDB: C:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc C  12 SRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    21        31        41        51        61        71        81        91       101       111    | |121    |  131       141       151       161  |    171       181       191       201       211
                                                                                                                                  116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                    118-MSE

Chain D from PDB  Type:PROTEIN  Length:201
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locd1 D:11-85 Hypothetical transcriptional regulator YcdC                d3locd2 D:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: D:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc D  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE

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 '\|'

(no "CATH Domain" information available for 3LOC, only for superseded entry 1PB6 replaced by 3LOC)

(no "Pfam Domain" information available for 3LOC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RUTR_ECOLI | P0ACU2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases 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.

Asymmetric Unit
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	3loc
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	RUTR_ECOLI \| P0ACU2	:	4jyk 4x1e 4xk4

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 20)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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