1KU9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY STRUCTURE OF A METHANOCOCCUS JANNASCHII DNA-BINDING PROTEIN: IMPLICATIONS FOR ANTIBIOTIC RESISTANCE IN STAPHYLOCOCCUS AUREUS

Authors :   S. S. Ray, J. B. Bonanno, H. Chen, H. De Lencastre, S. Wu, A. Tomasz, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   21 Jan 02 (Deposition) - 25 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Putative Transcription Factor, Homodimeric Winged-Helix Fold, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Ray, J. B. Bonanno, H. Chen, H. De Lencastre, S. Wu, A. Tomasz, S. K. Burley
X-Ray Structure Of An M. Jannaschii Dna-Binding Protein: Implications For Antibiotic Resistance In S. Aureus
Proteins V. 50 170 2002
PubMed-ID: 12471609 | Reference-DOI: 10.1002/PROT.10272
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN MJ223
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSKB2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ223
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Other Details	:	NYSGRC TARGET T088
	Synonym	:	HYPOTHETICAL PROTEIN MJ1563

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1KU9)

(no "SS Bond" information available for 1KU9)

(no "Cis Peptide Bond" information available for 1KU9)

(no "SAP(SNP)/Variant" information available for 1KU9)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	Y1563_METJA	7-106	2	A:7-106 B:1007-1106

(no "Exon" information available for 1KU9)

Asymmetric/Biological 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:151
 aligned with Y1563_METJA | Q58958 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Y1563_METJA      1 MIIMEEAKKLIIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSIKDIAKRKHDLIAKTYEDLKKLEEKCNEEEKEFIKQKIKGIERMKKISEKILEALNDLD  151
               SCOP domains d1ku9a_ A: DNA-binding protein Mj223                                                                                                                    SCOP domains
               CATH domains -1ku9A01 A:2-87 'winged helix' repressor DNA binding domain                            1ku9A02 A:88-151 Helix hairpin bin                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HTH_ARSR_2  PDB: A:7-106 UniProt: 7-106                                                             --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ku9 A    1 mIImEEAKKLIIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDImEELKISKGNVSmSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSIKDIAKRKHDLIAKTYEDLKKLEEKCNEEEKEFIKQKIKGIERmKKISEKILEALNDLD  151
                            |  |    10        20        30        40       |50        60        70        80        90       100       110       120       130     | 140       150 
                            |  |                                          48-MSE      60-MSE                                                                     136-MSE           
                            1-MSE                                                                                                                                                  
                               4-MSE

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Y1563_METJA | Q58958 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Y1563_METJA      1 MIIMEEAKKLIIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSIKDIAKRKHDLIAKTYEDLKKLEEKCNEEEKEFIKQKIKGIERMKKISEKILEALNDLD  151
               SCOP domains d1ku9b_ B: DNA-binding protein Mj223                                                                                                                    SCOP domains
               CATH domains -1ku9B01 B:1002-1088 'winged helix' repressor DNA binding domain                        1ku9B02 B:1089-1151 Helix hairpin bin                           CATH domains
           Pfam domains (1) --------------------------HTH_5-1ku9B01 B:1027-1073                      ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------HTH_5-1ku9B02 B:1027-1073                      ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HTH_ARSR_2  PDB: B:1007-1106 UniProt: 7-106                                                         --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ku9 B 1001 mIImEEAKKLIIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDImEELKISKGNVSmSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSIKDIAKRKHDLIAKTYEDLKKLEEKCNEEEKEFIKQKIKGIERmKKISEKILEALNDLD 1151
                            |  |  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130     |1140      1150 
                         1001-MSE                                       1048-MSE    1060-MSE                                                                    1136-MSE           
                            1004-MSE

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/Biological 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: All alpha proteins (14657)

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

Superfamily: Winged helix DNA-binding domain (576)

Family: DNA-binding protein Mj223 (1)

Protein domain: DNA-binding protein Mj223 (1)

Methanococcus jannaschii [TaxId: 2190] (1)

1a	d1ku9a_	A:
1b	d1ku9b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

1a	1ku9A01	A:2-87
1b	1ku9B01	B:1002-1088

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (4)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

2a	1ku9A02	A:88-151
2b	1ku9B02	B:1089-1151

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

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Clan: HTH (544)

Family: HTH_5 (8)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (1)

1a	HTH_5-1ku9B01	B:1027-1073
1b	HTH_5-1ku9B02	B:1027-1073

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Y1563_METJA | Q58958)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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: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/Biological Unit
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Ligands, Modified Residues, Ions (1, 10)

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