2P5L - JenaLib

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Title :   CRYSTAL STRUCTURE OF A DIMER OF N-TERMINAL DOMAINS OF AHRC IN COMPLEX WITH AN 18BP DNA OPERATOR SITE

Authors :   J. A. Garnett, F. Marincs, S. Baumberg, P. G. Stockley, S. E. V. Phillips

Date :   15 Mar 07 (Deposition) - 11 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Dna-Binding Domain, Winged Helix-Turn-Helix, Arg Box, Protein-Dna Complex, Transcription Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Garnett, F. Marincs, S. Baumberg, P. G. Stockley, S. E. Phillips
Structure And Function Of The Arginine Repressor-Operator Complex From Bacillus Subtilis.
J. Mol. Biol. V. 379 284 2008
PubMed-ID: 18455186 | Reference-DOI: 10.1016/J.JMB.2008.03.007

*Molecule 1 - DNA (5'- D(DCPDAPDTPDGPDAPDAPDTPDAPDAPDAPDAPDAPDTPDTPDCPDAPDA PDG)-3')*
	Chains	:	A, E
	Engineered	:	YES
	Other Details	:	SYNTHESIZED BY MWG-BIOTECH
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(DCPDTPDTPDGPDAPDAPDTPDTPDTPDTPDTPDAPDTPDTPDCPDAPDT PDG)-3')*
	Chains	:	B, F
	Engineered	:	YES
	Other Details	:	SYNTHESIZED BY MWG-BIOTECH
	Synthetic	:	YES

Molecule 3 - ARGININE REPRESSOR
	Chains	:	C, D, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	ARGR, AHRC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	ARGININE HYDROXAMATE RESISTANCE PROTEIN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS H:7 , ARG H:11 , LEU H:48	BINDING SITE FOR RESIDUE SO4 H 101
2	AC2	SOFTWARE	HIS G:7 , ARG G:11 , LEU G:48	BINDING SITE FOR RESIDUE SO4 G 102
3	AC3	SOFTWARE	THR D:55 , ASN D:56 , ASN D:57	BINDING SITE FOR RESIDUE SO4 D 103
4	AC4	SOFTWARE	LYS C:9 , TYR C:34 , THR H:55 , ASN H:56 , LYS H:61	BINDING SITE FOR RESIDUE SO4 H 104
5	AC5	SOFTWARE	ASN H:2 , LYS H:3 , GLY H:4 , GLN H:5	BINDING SITE FOR RESIDUE SO4 H 105

(no "SS Bond" information available for 2P5L)

(no "Cis Peptide Bond" information available for 2P5L)

(no "SAP(SNP)/Variant" information available for 2P5L)

(no "PROSITE Motif" information available for 2P5L)

(no "Exon" information available for 2P5L)

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:DNA  Length:18
                                                 
                  2p5l A  1 CATGAATAAAAATTCAAG 18
                                    10

Chain B from PDB  Type:DNA  Length:18
                                                 
                  2p5l B  1 CTTGAATTTTTATTCATG 18
                                    10

Chain C from PDB  Type:PROTEIN  Length:63
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:63
                                    11        21        31        41        51        61   
            ARGR_BACSU    2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
               SCOP domains d2p5lc1 C:2-64                                                  SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhh.eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2p5l C  2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
                                    11        21        31        41        51        61

Chain D from PDB  Type:PROTEIN  Length:64
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:64
                                    10        20        30        40        50        60    
            ARGR_BACSU    1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
               SCOP domains -d2p5ld1 D:2-64                                                  SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhh.eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  2p5l D  1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
                                    10        20        30        40        50        60

Chain E from PDB  Type:DNA  Length:18
                                                 
                  2p5l E  1 CATGAATAAAAATTCAAG 18
                                    10

Chain F from PDB  Type:DNA  Length:17
                                                
                  2p5l F  2 TTGAATTTTTATTCATG 18
                                    11

Chain G from PDB  Type:PROTEIN  Length:63
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:63
                                    11        21        31        41        51        61   
            ARGR_BACSU    2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
               SCOP domains d2p5lg1 G:2-64                                                  SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhh..eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2p5l G  2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
                                    11        21        31        41        51        61

Chain H from PDB  Type:PROTEIN  Length:64
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:64
                                    10        20        30        40        50        60    
            ARGR_BACSU    1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
               SCOP domains -d2p5lh1 H:2-64                                                  SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
           Pfam domains (1) Arg_repressor-2p5lH01 H:1-64                                     Pfam domains (1)
           Pfam domains (2) Arg_repressor-2p5lH02 H:1-64                                     Pfam domains (2)
           Pfam domains (3) Arg_repressor-2p5lH03 H:1-64                                     Pfam domains (3)
           Pfam domains (4) Arg_repressor-2p5lH04 H:1-64                                     Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhh.eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  2p5l H  1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSL 64
                                    10        20        30        40        50        60

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: Arginine repressor (ArgR), N-terminal DNA-binding domain (5)

Protein domain: Arginine repressor (ArgR), N-terminal DNA-binding domain (5)

Bacillus subtilis [TaxId: 1423] (3)

1a	d2p5lc1	C:2-64
1b	d2p5lh1	H:2-64
1c	d2p5ld1	D:2-64
1d	d2p5lg1	G:2-64

(no "CATH Domain" information available for 2P5L)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Arg_repressor (3)

Bacillus subtilis (2)

1a	Arg_repressor-2p5lH01	H:1-64
1b	Arg_repressor-2p5lH02	H:1-64
1c	Arg_repressor-2p5lH03	H:1-64
1d	Arg_repressor-2p5lH04	H:1-64

Asymmetric Unit(hide GO term definitions)

Chain C,D,G,H (ARGR_BACSU | P17893)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0034618	arginine binding	Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006526	arginine biosynthetic process	The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0019547	arginine catabolic process to ornithine	The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
	GO:0006525	arginine metabolic process	The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Cis Peptide Bonds" information available for 2p5l)

Biological Units
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	2p5l
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	ARGR_BACSU \| P17893	:	1f9n 2p5k 2p5m

2p5k	N-TERMINAL DOMAIN OF AHRC
2p5l	C-TERMINAL DOMAIN HEXAMER OF AHRC BOUND WITH L-ARGININE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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