2ER8 | PD0740 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LEU3 DNA-BINDING DOMAIN COMPLEXED WITH A 12MER DNA DUPLEX

Authors :   M. X. Fitzgerald, R. Marmorstein

Date :   24 Oct 05 (Deposition) - 04 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Zn(2)Cys(6) Binuclear Cluster Motif, Transcription Activator/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. X. Fitzgerald, J. R. Rojas, J. M. Kim, G. B. Kohlhaw, R. Marmorstein
Structure Of A Leu3-Dna Complex: Recognition Of Everted Cgg Half-Sites By A Zn2Cys6 Binuclear Cluster Protein.
Structure V. 14 725 2006
PubMed-ID: 16615914 | Reference-DOI: 10.1016/J.STR.2005.11.025
(for further references see the PDB file header)

*Molecule 1 - 5'-D(CPCPCPGPGPTPAPCPCPGPGPG)-3'*
	Chains	:	E, F, G, H
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - REGULATORY PROTEIN LEU3
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 32-103
	Gene	:	LEU3 (32-103)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B			E	F
Biological Unit 2 (1x)	:			C	D			G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:37 , CYS A:57 , CYS A:60 , CYS A:67 , ZN A:105	BINDING SITE FOR RESIDUE ZN A 104
2	AC2	SOFTWARE	CYS A:37 , CYS A:40 , CYS A:47 , CYS A:57 , ZN A:104	BINDING SITE FOR RESIDUE ZN A 105
3	AC3	SOFTWARE	CYS B:37 , CYS B:57 , CYS B:60 , CYS B:67 , ZN B:105	BINDING SITE FOR RESIDUE ZN B 104
4	AC4	SOFTWARE	CYS B:37 , CYS B:40 , CYS B:47 , CYS B:57 , ZN B:104	BINDING SITE FOR RESIDUE ZN B 105
5	AC5	SOFTWARE	CYS C:37 , CYS C:57 , CYS C:60 , CYS C:67 , ZN C:106	BINDING SITE FOR RESIDUE ZN C 105
6	AC6	SOFTWARE	CYS C:37 , CYS C:40 , CYS C:47 , CYS C:57 , ZN C:105	BINDING SITE FOR RESIDUE ZN C 106
7	AC7	SOFTWARE	CYS D:37 , CYS D:57 , CYS D:60 , CYS D:67 , ZN D:108	BINDING SITE FOR RESIDUE ZN D 107
8	AC8	SOFTWARE	CYS D:37 , CYS D:40 , CYS D:47 , CYS D:57 , ZN D:107	BINDING SITE FOR RESIDUE ZN D 108

(no "SS Bond" information available for 2ER8)

(no "Cis Peptide Bond" information available for 2ER8)

(no "SAP(SNP)/Variant" information available for 2ER8)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZN2_CY6_FUNGAL_1	PS00463	Zn(2)-C6 fungal-type DNA-binding domain signature.	LEUR_YEAST	36-67	4	A:36-67 B:36-67 C:36-67 D:36-67
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	LEUR_YEAST	36-69	4	A:36-69 B:36-69 C:36-69 D:36-69

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZN2_CY6_FUNGAL_1	PS00463	Zn(2)-C6 fungal-type DNA-binding domain signature.	LEUR_YEAST	36-67	2	A:36-67 B:36-67 - -
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	LEUR_YEAST	36-69	2	A:36-69 B:36-69 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZN2_CY6_FUNGAL_1	PS00463	Zn(2)-C6 fungal-type DNA-binding domain signature.	LEUR_YEAST	36-67	2	- - C:36-67 D:36-67
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	LEUR_YEAST	36-69	2	- - C:36-69 D:36-69

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR451W	1	YLR451W.1	XII:1036090-1038750	2661	LEUR_YEAST	1-886	886	4	A:32-99 B:33-99 C:33-96 D:32-99	68 67 64 68

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:68
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:68
                                    41        51        61        71        81        91        
            LEUR_YEAST   32 KRKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.....hhhhh...hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ZN2_CY6_FUNGAL_1  PDB: A:36-67  -------------------------------- PROSITE (1)
                PROSITE (2) ----ZN2_CY6_FUNGAL_2  PDB: A:36-69    ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:32-99 UniProt: 1-886 [INCOMPLETE]                   Transcript 1
                  2er8 A 32 KRKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
                                    41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:67
                                    42        52        62        72        82        92       
            LEUR_YEAST   33 RKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh....hhhhhh...hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_1  PDB: B:36-67  -------------------------------- PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_2  PDB: B:36-69    ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:33-99 UniProt: 1-886 [INCOMPLETE]                  Transcript 1
                  2er8 B 33 RKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
                                    42        52        62        72        82        92

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:64
                                    42        52        62        72        82        92    
            LEUR_YEAST   33 RKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTL 96
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.............hhhhhh..............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_1  PDB: C:36-67  ----------------------------- PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_2  PDB: C:36-69    --------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:33-96 UniProt: 1-886 [INCOMPLETE]               Transcript 1
                  2er8 C 33 RKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTL 96
                                    42        52        62        72        82        92

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:68
                                    41        51        61        71        81        91        
            LEUR_YEAST   32 KRKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....hhhhhh...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ZN2_CY6_FUNGAL_1  PDB: D:36-67  -------------------------------- PROSITE (1)
                PROSITE (2) ----ZN2_CY6_FUNGAL_2  PDB: D:36-69    ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:32-99 UniProt: 1-886 [INCOMPLETE]                   Transcript 1
                  2er8 D 32 KRKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
                                    41        51        61        71        81        91

Chain E from PDB  Type:DNA  Length:12
                                           
                  2er8 E  1 CCCGGTACCGGG 12
                                    10

Chain F from PDB  Type:DNA  Length:12
                                           
                  2er8 F 13 CCCGGTACCGGG 24
                                    22

Chain G from PDB  Type:DNA  Length:12
                                           
                  2er8 G  1 CCCGGTACCGGG 12
                                    10

Chain H from PDB  Type:DNA  Length:12
                                           
                  2er8 H 13 CCCGGTACCGGG 24
                                    22

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 "SCOP Domain" information available for 2ER8)

(no "CATH Domain" information available for 2ER8)

(no "Pfam Domain" information available for 2ER8)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LEUR_YEAST | P08638)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0001078	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009082	branched-chain amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009098	leucine biosynthetic process	The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic acid.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:2001278	positive regulation of leucine biosynthetic process	Any process that activates or increases the frequency, rate or extent of leucine biosynthetic process.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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(no "Cis Peptide Bonds" information available for 2er8)

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	2er8
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	LEUR_YEAST \| P08638	:	2ere 2erg

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (1, 4)

Sequences/Alignments

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