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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THREE-DIMENSIONAL STRUCTURE OF S.AUREUS METHICILLIN-RESISTANCE REGULATING TRANSCRIPTIONAL REPRESSOR MECI IN COMPLEX WITH 25-BP DS-DNA

Authors :   R. Garcia-Castellanos, G. Mallorqui-Fernandez, A. Marrero, J. Potem M. Coll, F. X. Gomis-Ruth

Date :   09 Feb 04 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Winged Helix-Turn-Helix, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Garcia-Castellanos, G. Mallorqui-Fernandez, A. Marrero, J. Potempa, M. Coll, F. X. Gomis-Ruth
On The Transcriptional Regulation Of Methicillin Resistance Meci Repressor In Complex With Its Operator
J. Biol. Chem. V. 279 17888 2004
PubMed-ID: 14960592 | Reference-DOI: 10.1074/JBC.M313123200
(for further references see the PDB file header)

Molecule 1 - 5'-D(GCTCCGATATTACAGTTGTAATTTT)-3'
	Chains	:	C
	Engineered	:	YES
	Other Details	:	MECI OPERATOR SEQUENCE
	Synthetic	:	YES

Molecule 2 - 5'-D(CAAAATTACAACTGTAATATCGGAG)-3'
	Chains	:	D
	Engineered	:	YES
	Other Details	:	MECI OPERATOR SEQUENCE
	Synthetic	:	YES

Molecule 3 - METHICILLIN RESISTANCE REGULATORY PROTEIN MECI
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX HTA (INVITROGEN)
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MECI
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	158879
	Strain	:	N315
	Synonym	:	METHICILLIN REPRESSOR MECI; MECI

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:112	BINDING SITE FOR RESIDUE K B 124

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

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

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

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

(no "Exon" information available for 1SAX)

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
	(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:120
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           MECI_STAAN     3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
               SCOP domains d1saxa_ A: Methicillin resistance regulatory protein MecI                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sax A   3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain A from PDB  Type:PROTEIN  Length:120
 aligned with MECI_STAAU | P68262 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           MECI_STAAU     3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
               SCOP domains d1saxa_ A: Methicillin resistance regulatory protein MecI                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sax A   3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           MECI_STAAN     3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
               SCOP domains d1saxb_ B: Methicillin resistance regulatory protein MecI                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----Pencillinase_R-1saxB01 B:8-122                                                                                      Pfam domains (1)
           Pfam domains (2) -----Pencillinase_R-1saxB02 B:8-122                                                                                      Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhh.eehhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sax B   3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with MECI_STAAU | P68262 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           MECI_STAAU     3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
               SCOP domains d1saxb_ B: Methicillin resistance regulatory protein MecI                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----Pencillinase_R-1saxB01 B:8-122                                                                                      Pfam domains (1)
           Pfam domains (2) -----Pencillinase_R-1saxB02 B:8-122                                                                                      Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhh.eehhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sax B   3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNK 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain C from PDB  Type:DNA  Length:25
                                                         
                 1sax C   1 GCTCCGATATTACAGTTGTAATTTT  25
                                    10        20

Chain D from PDB  Type:DNA  Length:25
                                                         
                 1sax D   1 CAAAATTACAACTGTAATATCGGAG  25
                                    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/Biological 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: Penicillinase repressor (10)

Protein domain: Methicillin resistance regulatory protein MecI (5)

Staphylococcus aureus [TaxId: 1280] (5)

1a	d1saxa_	A:
1b	d1saxb_	B:

(no "CATH Domain" information available for 1SAX)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Pencillinase_R (8)

Staphylococcus aureus (strain N315) (2)

1a	Pencillinase_R-1saxB01	B:8-122
1b	Pencillinase_R-1saxB02	B:8-122

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MECI_STAAU | P68262)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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.

Chain A,B (MECI_STAAN | P68261)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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.

Asymmetric/Biological Unit
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	1sax
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	MECI_STAAN \| P68261
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	MECI_STAAU \| P68262
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UniProtKB/Swiss-Prot
	MECI_STAAN \| P68261	:	1okr 1sd6 1sd7 2d45
	MECI_STAAU \| P68262	:	1okr 1sd6 1sd7

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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