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Title :   CRYSTAL STRUCTURE OF ACTIVATED BINARY COMPLEX OF HUTP, AN RNA BINDING ANTI-TERMINATION PROTEIN

Authors :   T. S. Kumarevel, H. Mizuno, P. K. R. Kumar

Date :   14 Sep 04 (Deposition) - 15 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hutp, Rna Binding, Antitermination, Transcription Regulation, L- Histidine, Conformational Change, Allosteric Activation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kumarevel, H. Mizuno, P. K. Kumar
Structural Basis Of Hutp-Mediated Anti-Termination And Role Of The Mg2+ Ion And L-Histidine Ligand.
Nature V. 434 183 2005
PubMed-ID: 15758992 | Reference-DOI: 10.1038/NATURE03355
(for further references see the PDB file header)

Molecule 1 - HUT OPERON POSITIVE REGULATORY PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET5A, PETHP4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	HUTP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	HIS	3	Mod. Amino Acid	HISTIDINE
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	HIS	6	Mod. Amino Acid	HISTIDINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:138 , HIS A:1001 , HIS C:73 , HIS C:77 , HOH C:3002	BINDING SITE FOR RESIDUE MG C 1002
2	AC2	SOFTWARE	HIS A:73 , HIS A:77 , HIS A:2001 , HOH A:2003 , HIS B:138	BINDING SITE FOR RESIDUE MG A 2002
3	AC3	SOFTWARE	HIS B:73 , HIS B:77 , HOH B:3003 , HIS C:138 , HIS C:3001	BINDING SITE FOR RESIDUE MG B 3002
4	AC4	SOFTWARE	ARG A:88 , ARG A:98 , ILE A:129 , GLY A:130 , ALA A:131 , HIS A:138 , TYR C:69 , TYR C:76 , HIS C:77 , MG C:1002	BINDING SITE FOR RESIDUE HIS A 1001
5	AC5	SOFTWARE	TYR A:69 , TYR A:76 , HIS A:77 , MG A:2002 , ARG B:88 , ARG B:98 , ILE B:129 , GLY B:130 , ALA B:131 , HIS B:138 , HOH B:3015	BINDING SITE FOR RESIDUE HIS A 2001
6	AC6	SOFTWARE	TYR B:69 , TYR B:76 , HIS B:77 , MG B:3002 , ARG C:88 , ARG C:98 , ILE C:129 , GLY C:130 , ALA C:131 , HIS C:138 , HOH C:3003	BINDING SITE FOR RESIDUE HIS C 3001

(no "SS Bond" information available for 1WPV)

(no "Cis Peptide Bond" information available for 1WPV)

(no "SAP(SNP)/Variant" information available for 1WPV)

(no "PROSITE Motif" information available for 1WPV)

(no "Exon" information available for 1WPV)

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
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Chain A from PDB  Type:PROTEIN  Length:147
 aligned with HUTP_BACSU | P10943 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           HUTP_BACSU     2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
               SCOP domains d1wpva_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 1wpvA00 A:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh......hhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpv A   2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with HUTP_BACSU | P10943 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           HUTP_BACSU     2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
               SCOP domains d1wpvb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 1wpvB00 B:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.....hhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpv B   2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with HUTP_BACSU | P10943 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           HUTP_BACSU     2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
               SCOP domains d1wpvc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains 1wpvC00 C:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
           Pfam domains (1) ------HutP-1wpvC01 C:8-146                                                                                                                       -- Pfam domains (1)
           Pfam domains (2) ------HutP-1wpvC02 C:8-146                                                                                                                       -- Pfam domains (2)
           Pfam domains (3) ------HutP-1wpvC03 C:8-146                                                                                                                       -- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpv C   2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Hut operon positive regulatory protein HutP (13)

Superfamily: Hut operon positive regulatory protein HutP (13)

Family: Hut operon positive regulatory protein HutP (13)

Protein domain: automated matches (10)

Bacillus subtilis [TaxId: 1423] (8)

1a	d1wpva_	A:
1b	d1wpvb_	B:
1c	d1wpvc_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Hut operon positive regulatory protein HutP (11)

Homologous Superfamily: Hut operon positive regulatory protein HutP (11)

Bacillus subtilis. Organism_taxid: 1423. (6)

1a	1wpvA00	A:2-148
1b	1wpvB00	B:2-148
1c	1wpvC00	C:2-148

Asymmetric Unit

Clans(

)

Families(

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Organisms( (-)

)

Clan: no clan defined [family: HutP] (9)

Family: HutP (9)

Bacillus subtilis (9)

1a	HutP-1wpvC01	C:8-146
1b	HutP-1wpvC02	C:8-146
1c	HutP-1wpvC03	C:8-146

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (HUTP_BACSU | P10943)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
	GO:0006547	histidine metabolic process	The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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.

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Biological Unit
	Complete Structure
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	1wpv
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	HUTP_BACSU \| P10943
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	HUTP_BACSU \| P10943
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UniProtKB/Swiss-Prot
	HUTP_BACSU \| P10943	:	1vea 1wmq 1wps 1wpt 1wpu 1wrn 1wro 1wrq 3boy 4h4l

1vea	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE ANALOG
1wmq	THE SAME PROTEIN COMPLEXED WITH METAL IONS, L-HISTIDINE AND 21-MER RNA
1wps	THE SAME PROTEIN CRYSTALLIZED IN THE PRESENCE OF A CHELATING AGENT, EDTA
1wpt	THE SAME PROTEIN CRYSTALLIZED IN THE PRESENCE OF MGCL2
1wpu	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND 21-MER RNA CONTAINING GAG REPEATS IN THE PRESENCE OF MGCL2

Description

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