3LGH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NIKR FROM HELICOBACTER PYLORI WITH VARIABLE NI SITE COORDINATION

Authors :   E. Pozharski, F. St John

Date :   20 Jan 10 (Deposition) - 15 Sep 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.37

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

Keywords :   Nikr, Nickel Coordination, Helicobacter Pylori, Octahedral, Square Planar, Dna-Binding, Metal-Binding, Nickel, Transcription, Transcription Regulation, Metal Binding Protein, Square Pyramidal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. West, F. St John, P. E. Lopes, A. D. Mackerell, E. Pozharski, S. L. Michel
Holo-Ni(Ii)Hpnikr Is An Asymmetric Tetramer Containing Two Different Nickel-Binding Sites.
J. Am. Chem. Soc. V. 132 14447 2010
PubMed-ID: 20863122 | Reference-DOI: 10.1021/JA104118R

Molecule 1 - NICKEL-RESPONSIVE REGULATOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B+
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HP_1338, NIKR
	Organism Common	:	CAMPYLOBACTER PYLORI
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	NI	4	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:99 , HIS A:101 , CYS A:107 , HIS D:88	BINDING SITE FOR RESIDUE NI A 149
2	AC2	SOFTWARE	ASP A:73 , HIS A:75 , HIS A:105	BINDING SITE FOR RESIDUE MG A 150
3	AC3	SOFTWARE	HIS B:99 , HIS B:101 , CYS B:107 , HIS C:88	BINDING SITE FOR RESIDUE NI B 149
4	AC4	SOFTWARE	HIS B:88 , HOH B:170 , HOH B:171 , HIS C:74 , HIS C:101	BINDING SITE FOR RESIDUE NI C 149
5	AC5	SOFTWARE	HIS A:88 , HOH A:157 , HIS D:74 , HIS D:101 , HOH D:170 , HOH D:171	BINDING SITE FOR RESIDUE NI D 149

(no "SS Bond" information available for 3LGH)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:55	-	Glu A:56
2	Glu A:62	-	Ser A:63

(no "SAP(SNP)/Variant" information available for 3LGH)

(no "PROSITE Motif" information available for 3LGH)

(no "Exon" information available for 3LGH)

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:131
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:133
                                    19        29        39        49        59        69        79        89        99       109       119       129       139   
           NIKR_HELPY    10 IIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3lgha1 A:10-59 automated matches                 --d3lgha2 A:62-142 automated matches                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....--..eeeeeeeee.....hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lgh A  10 IIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNP--ESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    19        29        39        49        59  |     69        79        89        99       109       119       129       139   
                                                                            59 62

Chain B from PDB  Type:PROTEIN  Length:139
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:139
                                    18        28        38        48        58        68        78        88        98       108       118       128       138         
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
               SCOP domains d3lghb1 B:9-60 automated matches                    d3lghb2 B:61-147 automated matches                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---RHH_1-3lghB01 B:12-51                   ------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---RHH_1-3lghB02 B:12-51                   ------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh........eeeeeeeee.....hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lgh B   9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
                                    18        28        38        48        58        68        78        88        98       108       118       128       138

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:79
                                    73        83        93       103       113       123       133         
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3lghc_ C: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3lgh C  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    73        83        93       103       113       123       133

Chain D from PDB  Type:PROTEIN  Length:78
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:78
                                    73        83        93       103       113       123       133        
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d3lghd_ D: automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -NikR_C-3lghD01 D:65-141                                                       Pfam domains (1)
           Pfam domains (2) -NikR_C-3lghD02 D:65-141                                                       Pfam domains (2)
           Pfam domains (3) -NikR_C-3lghD03 D:65-141                                                       Pfam domains (3)
           Pfam domains (4) -NikR_C-3lghD04 D:65-141                                                       Pfam domains (4)
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 3lgh D  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    73        83        93       103       113       123       133

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: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: automated matches (13)

Protein domain: automated matches (13)

Helicobacter pylori [TaxId: 85962] (9)

1a	d3lgha1	A:10-59
1b	d3lghb1	B:9-60

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: automated matches (16)

Protein domain: automated matches (16)

Helicobacter pylori [TaxId: 85962] (9)

2a	d3lgha2	A:62-142
2b	d3lghb2	B:61-147
2c	d3lghc_	C:
2d	d3lghd_	D:

(no "CATH Domain" information available for 3LGH)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: NikR_C (7)

Helicobacter pylori (Campylobacter pylori) (4)

1a	NikR_C-3lghD01	D:65-141
1b	NikR_C-3lghD02	D:65-141
1c	NikR_C-3lghD03	D:65-141
1d	NikR_C-3lghD04	D:65-141

Clan: Met_repress (26)

Family: RHH_1 (8)

Helicobacter pylori (Campylobacter pylori) (5)

2a	RHH_1-3lghB01	B:12-51
2b	RHH_1-3lghB02	B:12-51

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NIKR_HELPY | O25896)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	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:0010045	response to nickel cation	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 a nickel cation stimulus.
	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
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		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Ala A:55 - Glu A:56	[ RasMol ]
		Glu A:62 - Ser A:63	[ RasMol ]

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	3lgh
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	NIKR_HELPY \| O25896
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	NIKR_HELPY \| O25896	:	2ca9 2cad 2caj 2wvb 2wvc 2wvd 2wve 2wvf 3pht 3qsi

(no "Related Entries Specified in the PDB File" available for 3LGH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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