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Title :   SOLUTION STRUCTURE OF THE THIRD KOW MOTIF OF TRANSCRIPTION ELONGATION FACTOR SPT5

Authors :   W. Tanabe, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   27 Apr 06 (Deposition) - 27 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Kow Motif, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Third Kow Motif Of Transcription Elongation Factor Spt5
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR SPT5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P060130-01
	Expression System Vector Type	:	PLASMID
	Fragment	:	KOW MOTIF
	Gene	:	SUPT5H
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	HSPT5, DRB SENSITIVITY-INDUCING FACTOR LARGE SUBUNIT, DSIF LARGE SUBUNIT, DSIF P160, TAT- COTRANSACTIVATOR 1 PROTEIN, TAT-CT1 PROTEIN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DO3)

(no "Site" information available for 2DO3)

(no "SS Bond" information available for 2DO3)

(no "Cis Peptide Bond" information available for 2DO3)

(no "SAP(SNP)/Variant" information available for 2DO3)

(no "PROSITE Motif" information available for 2DO3)

(no "Exon" information available for 2DO3)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:69
 aligned with SPT5H_HUMAN | O00267 from UniProtKB/Swiss-Prot  Length:1087

    Alignment length:175
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518     
          SPT5H_HUMAN   349 GGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQPEGIDLEVVTESTGKEREHNFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 523
               SCOP domains -----------------------------------------------------------------------------------------------------------------d2do3a1 A:462-523 Transcription elongation factor SPT5         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----...------------------------------------------------------...------------------------------------------------...............eeee.......eeeeeeee....eeeee.....eeee....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2do3 A 455 G----SSG------------------------------------------------------SSG------------------------------------------------EFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 523
                            |    | | -         -         -         -         -         -  | |    -         -         -         -         -   |   468       478       488       498       508       518     
                            |  456 |                                                    459 |                                              462                                                             
                          455    458                                                      461

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Translation proteins SH3-like domain (251)

Family: SPT5 KOW domain-like (1)

Protein domain: Transcription elongation factor SPT5 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2do3a1

A:462-523

(no "CATH Domain" information available for 2DO3)

(no "Pfam Domain" information available for 2DO3)

NMR Structure(hide GO term definitions)

Chain A (SPT5H_HUMAN | O00267)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006370	7-methylguanosine mRNA capping	Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
	GO:0006354	DNA-templated transcription, elongation	The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0032785	negative regulation of DNA-templated transcription, elongation	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	GO:1900364	negative regulation of mRNA polyadenylation	Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
	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:0032786	positive regulation of DNA-templated transcription, elongation	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	GO:0016239	positive regulation of macroautophagy	Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
	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:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	GO:0032784	regulation of DNA-templated transcription, elongation	Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	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:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0039692	single stranded viral RNA replication via double stranded DNA intermediate	A viral genome replication where the template is single-stranded RNA (ssRNA), and which proceeds via a double stranded DNA (dsDNA) intermediate molecule. Viral genomic RNA is first reverse transcribed into dsDNA, which integrates into the host chromosomal DNA, where it is transcribed by host RNA polymerase II.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	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:0032044	DSIF complex	A heterodimeric protein complex formed of Spt4 and Spt5 proteins which is expressed in eukaryotes from yeast to man. DSIF is an inhibitory elongation factor that promotes RNA polymerase II transcriptional pausing, but can also stimulate transcriptional elongation under certain conditions, and may play a role in RNA processing via its physical association with mRNA capping enzymes.
	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.

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