1MJO | PD0246 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT

Authors :   C. W. Garvie, S. E. V. Phillips

Date :   28 Jan 98 (Deposition) - 02 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transcription Regulation, Metj, Methionine Repressor, Sheet- Helix-Helix, S-Adenosyl Methionine, Dna, Complex (Transcription Regulation/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. W. Garvie, S. E. Phillips
Direct And Indirect Readout In Mutant Met Repressor-Operator Complexes.
Structure Fold. Des. V. 8 905 2000
PubMed-ID: 10986458 | Reference-DOI: 10.1016/S0969-2126(00)00182-9
(for further references see the PDB file header)

Molecule 1 - CONSENSUS DNA OPERATOR DUPLEX WITH THE CENTRAL TA STEP MUTATED TO AT
	Chains	:	F, G
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - METHIONINE REPRESSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	METJ
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SAM	4	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:90 , GLU A:94 , HOH A:272 , GLU B:90 , GLU B:94 , HOH B:1344 , HOH D:3367	BINDING SITE FOR RESIDUE CA B 202
2	AC2	SOFTWARE	GLU A:39 , ARG A:42 , ARG A:43 , LEU A:56 , GLU A:59 , ALA A:60 , HIS A:63 , PRO A:71 , HOH A:212 , HOH A:262 , HOH A:299 , HOH A:1304 , HOH A:1353 , HOH A:1395 , PHE B:61 , HIS B:63 , ALA B:64 , PHE B:65 , GLY B:67 , HOH B:1336	BINDING SITE FOR RESIDUE SAM A 199
3	AC3	SOFTWARE	PHE A:61 , HIS A:63 , ALA A:64 , PHE A:65 , GLY A:67 , HOH A:233 , HOH A:1353 , GLU B:39 , ARG B:43 , LEU B:56 , GLU B:59 , ALA B:60 , HIS B:63 , PRO B:71 , HOH B:218 , HOH B:245 , HOH B:1303 , HOH B:1355	BINDING SITE FOR RESIDUE SAM B 200
4	AC4	SOFTWARE	PHE C:61 , HIS C:63 , ALA C:64 , PHE C:65 , GLY C:67 , HOH C:2331 , HOH C:2344 , HOH C:3346 , HOH C:3373 , GLU D:39 , ARG D:42 , ARG D:43 , LEU D:56 , GLU D:59 , ALA D:60 , HIS D:63 , PRO D:71	BINDING SITE FOR RESIDUE SAM C 200
5	AC5	SOFTWARE	GLU C:39 , ARG C:42 , ARG C:43 , LEU C:56 , GLU C:59 , HIS C:63 , PRO C:71 , PHE D:61 , HIS D:63 , ALA D:64 , PHE D:65 , GLY D:67 , HOH D:2324 , HOH D:2348 , HOH D:2366 , HOH D:3337 , HOH D:3366	BINDING SITE FOR RESIDUE SAM D 200

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

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

Asymmetric/Biological Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_METJ_ECOLI_001 *	L	57	Q	METJ_ECOLI	---	---	A/B/C/D	L	56	Q
2	UniProt	VAR_METJ_ECOLI_002 *	A	61	T	METJ_ECOLI	---	---	A/B/C/D	A	60	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 1MJO)

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:104
 aligned with METJ_ECOLI | P0A8U6 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           METJ_ECOLI     2 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 105
               SCOP domains d1mjoa_ A: Met repressor, MetJ (MetR)                                                                    SCOP domains
               CATH domains 1mjoA00 A:1-104 MET Apo-Repressor, subunit A                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...................hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------Q---T-------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1mjo A   1 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 104
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with METJ_ECOLI | P0A8U6 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           METJ_ECOLI     2 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 105
               SCOP domains d1mjob_ B: Met repressor, MetJ (MetR)                                                                    SCOP domains
               CATH domains 1mjoB00 B:1-104 MET Apo-Repressor, subunit A                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...................hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------Q---T-------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1mjo B   1 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 104
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with METJ_ECOLI | P0A8U6 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           METJ_ECOLI     2 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 105
               SCOP domains d1mjoc_ C: Met repressor, MetJ (MetR)                                                                    SCOP domains
               CATH domains 1mjoC00 C:1-104 MET Apo-Repressor, subunit A                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...................hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------Q---T-------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1mjo C   1 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 104
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:104
 aligned with METJ_ECOLI | P0A8U6 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           METJ_ECOLI     2 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 105
               SCOP domains d1mjod_ D: Met repressor, MetJ (MetR)                                                                    SCOP domains
               CATH domains 1mjoD00 D:1-104 MET Apo-Repressor, subunit A                                                             CATH domains
           Pfam domains (1) MetJ-1mjoD01 D:1-103                                                                                   - Pfam domains (1)
           Pfam domains (2) MetJ-1mjoD02 D:1-103                                                                                   - Pfam domains (2)
           Pfam domains (3) MetJ-1mjoD03 D:1-103                                                                                   - Pfam domains (3)
           Pfam domains (4) MetJ-1mjoD04 D:1-103                                                                                   - Pfam domains (4)
         Sec.struct. author ....................eeeeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...................hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------Q---T-------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1mjo D   1 AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY 104
                                    10        20        30        40        50        60        70        80        90       100

Chain F from PDB  Type:DNA  Length:19
                                                   
                 1mjo F  -1 TTAGACGTCATGACGTCTA  17
                                     8

Chain G from PDB  Type:DNA  Length:19
                                                   
                 1mjo G  -1 TTAGACGTCATGACGTCTA  17
                                     8

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(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: Met repressor, MetJ (MetR) (10)

Protein domain: Met repressor, MetJ (MetR) (10)

Escherichia coli [TaxId: 562] (10)

1a	d1mjoa_	A:
1b	d1mjoc_	C:
1c	d1mjod_	D:
1d	d1mjob_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: MET Apo-Repressor, subunit A (10)

Homologous Superfamily: MET Apo-Repressor, subunit A (10)

[unclassified] (6)

1a	1mjoA00	A:1-104
1b	1mjoB00	B:1-104
1c	1mjoC00	C:1-104
1d	1mjoD00	D:1-104

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Met_repress (26)

Family: MetJ (6)

Escherichia coli (strain K12) (6)

1a	MetJ-1mjoD01	D:1-103
1b	MetJ-1mjoD02	D:1-103
1c	MetJ-1mjoD03	D:1-103
1d	MetJ-1mjoD04	D:1-103

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (METJ_ECOLI | P0A8U6)

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: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:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0006555	methionine metabolic process	The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	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: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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1mjo
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	METJ_ECOLI \| P0A8U6	:	1cma 1cmb 1cmc 1mj2 1mjk 1mjl 1mjm 1mjp 1mjq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 8)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

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