1WRO - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   METAL ION DEPENDENCY OF THE ANTITERMINATOR PROTEIN, HUTP, FOR BINDING TO THE TERMINATOR REGION OF HUT MRNA- A STRUCTURAL BASIS

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

Date :   25 Oct 04 (Deposition) - 30 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

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

Reference :   T. Kumarevel, H. Mizuno, P. K. R. Kumar
Characterization Of The Metal Ion Binding Site In The Anti-Terminator Protein, Hutp, Of Bacillus Subtilis
Nucleic Acids Res. V. 33 5494 2005
PubMed-ID: 16192572 | Reference-DOI: 10.1093/NAR/GKI868
(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
	Expression System Strain	:	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, 9)

No.	Name	Count	Type	Full Name
1	BA	6	Ligand/Ion	BARIUM ION
2	HIS	3	Mod. Amino Acid	HISTIDINE

Biological Unit 1 (1, 6)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:138 , HIS A:1001 , HIS C:73 , HIS C:77 , HOH C:4002	BINDING SITE FOR RESIDUE BA C 4001
2	AC2	SOFTWARE	HIS A:73 , HIS A:77 , HOH A:4007 , HIS B:138 , HIS B:2001	BINDING SITE FOR RESIDUE BA A 4002
3	AC3	SOFTWARE	HIS B:73 , HIS B:77 , HOH B:4006 , HIS C:138 , HIS C:3001	BINDING SITE FOR RESIDUE BA B 4003
4	AC4	SOFTWARE	GLU A:90 , BA A:4006 , BA B:4005 , GLY C:89	BINDING SITE FOR RESIDUE BA A 4004
5	AC5	SOFTWARE	BA A:4004 , BA A:4006 , GLY B:89 , GLU B:90 , GLU C:90	BINDING SITE FOR RESIDUE BA B 4005
6	AC6	SOFTWARE	GLY A:89 , BA A:4004 , GLU B:90 , BA B:4005	BINDING SITE FOR RESIDUE BA A 4006
7	AC7	SOFTWARE	ARG A:88 , LEU A:97 , ARG A:98 , ILE A:129 , GLY A:130 , ALA A:131 , TYR C:69 , TYR C:76 , HIS C:77 , BA C:4001	BINDING SITE FOR RESIDUE HIS A 1001
8	AC8	SOFTWARE	TYR A:69 , TYR A:76 , HIS A:77 , BA A:4002 , ARG B:88 , ARG B:98 , ILE B:129 , GLY B:130 , ALA B:131 , HIS B:138	BINDING SITE FOR RESIDUE HIS B 2001
9	AC9	SOFTWARE	TYR B:69 , TYR B:76 , HIS B:77 , BA B:4003 , ARG C:88 , ARG C:98 , ILE C:129 , GLY C:130 , ALA C:131 , HIS C:138 , HOH C:4049	BINDING SITE FOR RESIDUE HIS C 3001

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

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

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

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

(no "Exon" information available for 1WRO)

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 d1wroa_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 1wroA00 A:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...hhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wro 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 d1wrob_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 1wroB00 B:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...hhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wro 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 d1wroc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains 1wroC00 C:2-148 Hut operon positive regulatory protein HutP                                                                                         CATH domains
           Pfam domains (1) ------HutP-1wroC01 C:8-146                                                                                                                       -- Pfam domains (1)
           Pfam domains (2) ------HutP-1wroC02 C:8-146                                                                                                                       -- Pfam domains (2)
           Pfam domains (3) ------HutP-1wroC03 C:8-146                                                                                                                       -- Pfam domains (3)
         Sec.struct. author ......hhhhhhhhhhhh.....hhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wro 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)
		→ 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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d1wroa_	A:
1b	d1wrob_	B:
1c	d1wroc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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	1wroA00	A:2-148
1b	1wroB00	B:2-148
1c	1wroC00	C:2-148

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: HutP (9)

Bacillus subtilis (9)

1a	HutP-1wroC01	C:8-146
1b	HutP-1wroC02	C:8-146
1c	HutP-1wroC03	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HIS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wro)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1wro
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HUTP_BACSU \| P10943
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HUTP_BACSU \| P10943
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HUTP_BACSU \| P10943	:	1vea 1wmq 1wps 1wpt 1wpu 1wpv 1wrn 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 CONTAINING UAG REPEATING MOTIFS
1wps	THE SAME PROTEIN CRYSTALLIZED IN THE PRESENCE OF CHELATING AGENT, EDTA
1wpt	THE SAME PROTEIN CRYSTALLIZED IN THE PRESENCE OF MGCL2
1wpu	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE, MGCL2 AND 21- MER RNA CONTAINING GAG REPEATING MOTIFS
1wpv	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND MGCL2
1wrn	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND MANGANESE ION
1wrq	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND MAGNESIUM ION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File