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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUTP ANTITERMINATION COMPLEX BOUND TO THE HUT MRNA

Authors :   T. S. Kumarevel, D. Balasundaresan, J. Jeyakanthan, A. Shinkai, S. Yokoyama, P. K. R. Kumar, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   18 Dec 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hutp, Rna-Binding, Hutp-Rna Complex, Anti-Termination, Transcription Regulation, Activator, Histidine Metabolism, Transcription/Rna Complex, 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. Kumarevel, D. Balasundaresan, J. Jeyakanthan, A. Shinkai, S. Yokoyama, P. K. R. Kumar
Crystal Structure Of Hutp Complexed With The 55-Mer Rna
To Be Published
PubMed: search
(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
	Gene	:	HUTP
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	HUTP

*Molecule 2 - 5'- R(UPUPUPAPGPUPUPUPUPUPAPGPUPUPUPUPUPAPGP UPUPU)-3'*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

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

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

(no "Site" information available for 3BOY)

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

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

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

(no "PROSITE Motif" information available for 3BOY)

(no "Exon" information available for 3BOY)

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: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 d3boya_ A: Hut operon positive regulatory protein HutP                                                                                              SCOP domains
               CATH domains 3boyA00 A: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
                 3boy 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 d3boyb_ B: Hut operon positive regulatory protein HutP                                                                                              SCOP domains
               CATH domains 3boyB00 B:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3boy 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 d3boyc_ C: Hut operon positive regulatory protein HutP                                                                                              SCOP domains
               CATH domains 3boyC00 C: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
                 3boy C   2 TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:DNA/RNA  Length:22
                                                      
                 3boy D   1 UUUAGUUUUUAGUUUUUAGUUU  22
                                    10        20

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 '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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. (2)

1a	3boyA00	A:2-148
1b	3boyB00	B:2-148
1c	3boyC00	C:2-148

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

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.

Asymmetric Unit
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	Sites
(no "Sites" information available for 3boy)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3boy)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3boy
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	HUTP_BACSU \| P10943
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		Domain Information	:	XDom
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	HUTP_BACSU \| P10943
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UniProtKB/Swiss-Prot
	HUTP_BACSU \| P10943	:	1vea 1wmq 1wps 1wpt 1wpu 1wpv 1wrn 1wro 1wrq 4h4l

1vea	CRYSTAL STRUCTURE OF THE HUTP COMPLEXED WITH L-HISTIDINE ANALOG
1wmq	CRYSTAL STRUCTURE OF THE HUTP-RNA COMPLEX
1wpt	CRYSTAL STRUCTURE OF HUTP
1wpu	CRYSTAL STRUCTURE OF THE HUTP BOUND TO THE RNA
1wpv	CRYSTAL STRUCTURE OF HUTP COMPLEX RELATED ID: AR_001000707.1 RELATED DB: TARGETDB
1wrq	CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF HUTP (HUTP-L- HISTIDINE-MG2+)

Description

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Ligands, Modified Residues, Ions (2, 6)

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