2Y3Y - JenaLib

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Title :   HOLO-NI(II) HPNIKR IS A SYMMETRIC TETRAMER CONTAINING FOUR CANONIC SQUARE-PLANAR NI(II) IONS AT PHYSIOLOGICAL PH

Authors :   S. Benini, M. Cianci, S. Ciurli

Date :   04 Jan 11 (Deposition) - 17 Aug 11 (Release) - 17 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym. Unit : A,B,C,D,Q
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: Q  (1x)

Keywords :   Transcription, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Benini, M. Cianci, S. Ciurli
Holo-Ni(2+)Helicobacter Pylori Nikr Contains Four Square-Planar Nickel-Binding Sites At Physiological Ph.
Dalton Trans V. 40 7831 2011
PubMed-ID: 21725560 | Reference-DOI: 10.1039/C1DT11107H

Molecule 1 - PUTATIVE NICKEL-RESPONSIVE REGULATOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET22B
	Fragment	:	C-TERMINAL METAL-BINDING DOMAIN, RESIDUES 58-145
	Organism Scientific	:	HELICOBACTER PYLORI G27
	Organism Taxid	:	563041
	Synonym	:	HOLO-NICKEL HPNIKR

Molecule 2 - UNDECAPEPTIDE-GSSSGSASGAG
	Chains	:	Q
	Organism Scientific	:	UNIDENTIFIED
	Organism Taxid	:	32644

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	Q
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	NI	4	Ligand/Ion	NICKEL (II) ION
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:99 , HIS A:101 , CYS A:107 , HIS B:88	BINDING SITE FOR RESIDUE NI A1143
2	AC2	SOFTWARE	HIS A:88 , HIS B:99 , HIS B:101 , CYS B:107	BINDING SITE FOR RESIDUE NI B1143
3	AC3	SOFTWARE	HIS C:99 , HIS C:101 , CYS C:107 , ILE D:84 , HIS D:88	BINDING SITE FOR RESIDUE NI C1142
4	AC4	SOFTWARE	PEG C:1145	BINDING SITE FOR RESIDUE PEG C1144
5	AC5	SOFTWARE	PEG C:1144 , PEG C:1146	BINDING SITE FOR RESIDUE PEG C1145
6	AC6	SOFTWARE	PEG C:1145	BINDING SITE FOR RESIDUE PEG C1146
7	AC7	SOFTWARE	HIS C:88 , HIS D:99 , HIS D:101 , CYS D:107	BINDING SITE FOR RESIDUE NI D1143

(no "SS Bond" information available for 2Y3Y)

(no "Cis Peptide Bond" information available for 2Y3Y)

(no "SAP(SNP)/Variant" information available for 2Y3Y)

(no "PROSITE Motif" information available for 2Y3Y)

(no "Exon" information available for 2Y3Y)

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:PROTEIN  Length:83
 aligned with NIKR_HELPG | B5Z8Y5 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:83
                                    69        79        89        99       109       119       129       139   
           NIKR_HELPG    60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d2y3ya_ A: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2y3y A  60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    69        79        89        99       109       119       129       139

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with NIKR_HELPG | B5Z8Y5 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:83
                                    69        79        89        99       109       119       129       139   
           NIKR_HELPG    60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d2y3yb_ B: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2y3y B  60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:81
 aligned with NIKR_HELPG | B5Z8Y5 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:81
                                    70        80        90       100       110       120       130       140 
           NIKR_HELPG    61 DESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d2y3yc_ C: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2y3y C  61 DESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:83
 aligned with NIKR_HELPG | B5Z8Y5 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:83
                                    69        79        89        99       109       119       129       139   
           NIKR_HELPG    60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d2y3yd_ D: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2y3y D  60 NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    69        79        89        99       109       119       129       139

Chain Q from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2y3y Q   1 GSSSGSASGAG  11
                                    10

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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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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: 563041] (2)

1a	d2y3ya_	A:
1b	d2y3yb_	B:
1c	d2y3yc_	C:
1d	d2y3yd_	D:

(no "CATH Domain" information available for 2Y3Y)

(no "Pfam Domain" information available for 2Y3Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NIKR_HELPG | B5Z8Y5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.

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	Cis Peptide Bonds
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	2y3y
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2ca9	APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION
2cad	NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES
2caj	NI2-HPNIKR HPNIKR IN CLOSED TRANS- CONFORMATION AND NICKEL BOUND TO 4 INTERMEDIARY SITES
2wvb	STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wvc	STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wvd	STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wve	STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wvf	STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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