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Title :   SOLUTION STRUCTURE OF THREE TANDEM REPEATS OF ZF-C2H2 DOMAINS FROM HUMAN KRUPPEL-LIKE FACTOR 5

Authors :   T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   09 Feb 07 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   C2H2-Type Zinc-Finger, Metal Bind, Transcription Factor, Kruppel-Like Factor, Gc-Box Promoter Elements, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of Three Tandem Repeats Of Zf-C2H2 Domains From Human Kruppel-Like Factor 5
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - KRUEPPEL-LIKE FACTOR 5
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060116-02
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZF-C2H2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	INTESTINAL-ENRICHED KRUEPPEL-LIKE FACTOR, COLON KRUEPPEL-LIKE FACTOR, TRANSCRIPTION FACTOR BTEB2, BASIC TRANSCRIPTION ELEMENT-BINDING PROTEIN 2, BTE-BINDING PROTEIN 2, GC BOX-BINDING PROTEIN 2


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

NMR Structure (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:375 , CYS A:380 , HIS A:393 , HIS A:397	BINDING SITE FOR RESIDUE ZN A 100
2	AC2	SOFTWARE	CYS A:405 , CYS A:410 , HIS A:423 , HIS A:427	BINDING SITE FOR RESIDUE ZN A 200
3	AC3	SOFTWARE	CYS A:435 , CYS A:438 , HIS A:451 , HIS A:455	BINDING SITE FOR RESIDUE ZN A 300

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

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

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

NMR Structure (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	KLF5_HUMAN	375-397 405-427 435-455	3	A:375-397 A:405-427 A:435-455

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000377687	2	ENSE00001474889	chr13:73632930-73633726	797	KLF5_HUMAN	1-87	87	0	-	-
1.4c	ENST00000377687	4c	ENSE00000683628	chr13:73635999-73636872	874	KLF5_HUMAN	88-379	292	1	A:358-379 (gaps)	75
1.5	ENST00000377687	5	ENSE00000683627	chr13:73637962-73638021	60	KLF5_HUMAN	379-399	21	1	A:379-399	21
1.7b	ENST00000377687	7b	ENSE00001474860	chr13:73649846-73651676	1831	KLF5_HUMAN	399-457	59	1	A:399-457	59

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:100
 aligned with KLF5_HUMAN | Q13887 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:153
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454   
           KLF5_HUMAN   305 PSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPVRYNRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGVCNRSFSRSDHLALHMKRHQN 457
               SCOP domains d2e  bt                                                   a_ A: automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--..---------------------------------------------------..........ee........ee.hhhhhhhhhhhhh....ee........ee.hhhhhhhhhhhhh...............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1   -- PROSITE
           Transcript 1 (1) Exon 1.4c  PDB: A:358-379 (gaps) UniProt: 88-379 [INCOMPLETE]              -------------------Exon 1.7b  PDB: A:399-457 UniProt: 399-457                  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.5             ---------------------------------------------------------- Transcript 1 (2)
                 2ebt A 358 GSS--GS---------------------------------------------------SGPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGVCNRSFSRSDHLALHMKRHQN 457
                              |  ||  -         -         -         -         -       364       374       384       394       404       414       424       434       444       454   
                              |  ||                                                 363                                                                                              
                            360  ||                                                                                                                                                  
                               361|                                                                                                                                                  
                                362

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: beta-beta-alpha zinc fingers (183)

Superfamily: beta-beta-alpha zinc fingers (183)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (2)

d2ebta_

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

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

NMR Structure(hide GO term definitions)

Chain A (KLF5_HUMAN | Q13887)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA 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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic 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.
	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.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0060576	intestinal epithelial cell development	The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.
	GO:0030033	microvillus assembly	Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
	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:0045600	positive regulation of fat cell differentiation	Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032534	regulation of microvillus assembly	A process that modulates the formation of a microvillus.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates 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:0035914	skeletal muscle cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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