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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 :   2.30

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 (3, 12)

No.	Name	Count	Type	Full Name
1	HIS	3	Mod. Amino Acid	HISTIDINE
2	MN	3	Ligand/Ion	MANGANESE (II) ION
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	HIS	6	Mod. Amino Acid	HISTIDINE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:138 , HIS A:1001 , HIS C:73 , HIS C:77 , HOH C:4046	BINDING SITE FOR RESIDUE MN C 4001
02	AC2	SOFTWARE	HIS A:73 , HIS A:77 , HOH A:4084 , HIS B:138 , HIS B:2001	BINDING SITE FOR RESIDUE MN A 4002
03	AC3	SOFTWARE	HIS B:73 , HIS B:77 , HOH B:4046 , HIS C:138 , HIS C:3001	BINDING SITE FOR RESIDUE MN B 4003
04	AC4	SOFTWARE	ARG A:88 , ARG A:98 , ILE A:129 , GLY A:130 , ALA A:131 , HIS A:138 , HOH A:4067 , TYR C:69 , TYR C:76 , HIS C:77 , MN C:4001	BINDING SITE FOR RESIDUE HIS A 1001
05	AC5	SOFTWARE	TYR A:69 , TYR A:76 , HIS A:77 , MN A:4002 , ARG B:88 , ARG B:98 , ILE B:129 , GLY B:130 , ALA B:131 , HIS B:138 , HOH B:4030	BINDING SITE FOR RESIDUE HIS B 2001
06	AC6	SOFTWARE	TYR B:69 , TYR B:76 , HIS B:77 , MN B:4003 , ARG C:88 , LEU C:97 , ARG C:98 , ILE C:129 , GLY C:130 , ALA C:131 , HIS C:138	BINDING SITE FOR RESIDUE HIS C 3001
07	AC7	SOFTWARE	GLU A:81 , ALA A:82 , HIS A:84 , GLY A:85 , ARG A:88 , PHE A:141 , GLY A:142 , VAL A:143	BINDING SITE FOR RESIDUE PEG A 3801
08	AC8	SOFTWARE	ALA A:116 , GLU A:117 , HOH A:4094 , GLN C:65 , GLU C:67 , GLY C:68 , TYR C:69 , ARG C:70 , GLU C:71 , ARG C:108	BINDING SITE FOR RESIDUE PEG A 3802
09	AC9	SOFTWARE	GLU A:23 , GLY B:62 , ILE B:64 , ARG B:108	BINDING SITE FOR RESIDUE PEG B 3803
10	BC1	SOFTWARE	MET A:45 , GLY A:94 , SER A:95 , HIS C:48	BINDING SITE FOR RESIDUE PEG A 3804
11	BC2	SOFTWARE	ARG C:11 , LEU C:12 , HOH C:4088	BINDING SITE FOR RESIDUE PEG C 3805
12	BC3	SOFTWARE	ILE A:51 , ILE A:54 , GLU A:55 , SER A:72 , LEU A:75 , TYR A:76 , THR A:79	BINDING SITE FOR RESIDUE PEG A 3806

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

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

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

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

(no "Exon" information available for 1WRN)

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:146
 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 d1wrna_ A: automated  matches                                                                                                                       SCOP domains
               CATH domains 1wrnA00 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..........eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrn A   2 TLHKERRIGRLSVLLLLNEA-ESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21 |      31        41        51        61        71        81        91       101       111       121       131       141       
                                              21 |                                                                                                                             
                                                23

Chain B from PDB  Type:PROTEIN  Length:146
 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 d1wrnb_ B: automated  matches                                                                                                                       SCOP domains
               CATH domains 1wrnB00 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
                 1wrn B   2 TLHKERRIGRLSVLLLLNEA-ESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        21 |      31        41        51        61        71        81        91       101       111       121       131       141       
                                              21 |                                                                                                                             
                                                23

Chain C from PDB  Type:PROTEIN  Length:143
 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 d1wrnc_ C: automate    d matches                                                                                                                    SCOP domains
               CATH domains 1wrnC00 C:2-148 Hut     operon positive regulatory protein HutP                                                                                     CATH domains
           Pfam domains (1) ------HutP-1wrnC01     C:8-146                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) ------HutP-1wrnC02     C:8-146                                                                                                                   -- Pfam domains (2)
           Pfam domains (3) ------HutP-1wrnC03     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
                 1wrn C   2 TLHKERRIGRLSVLLLLNE----TQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI 148
                                    11        |-   |    31        41        51        61        71        81        91       101       111       121       131       141       
                                             20   25

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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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	d1wrna_	A:
1b	d1wrnb_	B:
1c	d1wrnc_	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	1wrnC00	C:2-148
1b	1wrnA00	A:2-148
1c	1wrnB00	B:2-148

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: HutP (9)

Bacillus subtilis (9)

1a	HutP-1wrnC01	C:8-146
1b	HutP-1wrnC02	C:8-146
1c	HutP-1wrnC03	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
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Biological Unit
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	1wrn
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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 1wpv 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 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
1wro	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND BARIUM ION
1wrq	THE SAME PROTEIN COMPLEXED WITH L-HISTIDINE AND MAGNESIUM ION

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (6, 6)

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