2IIF | PD0879 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   SINGLE CHAIN INTEGRATION HOST FACTOR MUTANT PROTEIN (SCIHF2-K45AE) IN COMPLEX WITH DNA

Authors :   Q. Bao, P. Droege, C. A. Davey

Date :   28 Sep 06 (Deposition) - 20 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.72

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

Keywords :   Dna Kinking, Bending, U-Turn, Intercalation, Divalent, Metal, Recombination/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Bao, H. Chen, Y. Liu, J. Yan, P. Droge, C. A. Davey
A Divalent Metal-Mediated Switch Controlling Protein-Induced Dna Bending
J. Mol. Biol. V. 367 731 2007
PubMed-ID: 17276457 | Reference-DOI: 10.1016/J.JMB.2006.09.082
(for further references see the PDB file header)

Molecule 1 - PHAGE P H' SITE
	Chains	:	C
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(DGPDGPDCPDCPDAPDAPDAPDAPDAPDAPDGPDCPDAPDTP DT)-3')**
	Chains	:	D
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(DGPDCPDTPDTPDAPDTPDCPDAPDAPDTPDTPDTPDGPDTP DTPDGPDCPDAPDCPDC)-3')*
	Chains	:	E
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

Molecule 4 - INTEGRATION HOST FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	IHF-ALPHA, IHF-BETA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MN	8	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:161 , GLU A:172 , DT D:28 , HOH D:946	BINDING SITE FOR RESIDUE MN D 303
2	AC2	SOFTWARE	DA D:24 , HOH D:919 , HOH D:948	BINDING SITE FOR RESIDUE MN D 304
3	AC3	SOFTWARE	GLU A:174 , DG E:30 , HOH E:768 , HOH E:813	BINDING SITE FOR RESIDUE MN E 302
4	AC4	SOFTWARE	HIS A:155 , HOH A:716 , HOH A:789	BINDING SITE FOR RESIDUE MN A 301
5	AC5	SOFTWARE	ASN A:84 , HOH A:704 , DG C:-48 , HOH C:943	BINDING SITE FOR RESIDUE MN A 305
6	AC6	SOFTWARE	GLU A:54 , ASP A:58 , HOH A:756 , HOH A:886	BINDING SITE FOR RESIDUE MN A 306
7	AC7	SOFTWARE	HOH A:968 , HOH D:915	BINDING SITE FOR RESIDUE MN A 307
8	AC8	SOFTWARE	GLU A:89 , HOH A:840 , DT C:-21	BINDING SITE FOR RESIDUE MN A 308

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	IHFB_ECOLI	47-66	1	A:148-167
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	IHFA_ECOLI	48-67	1	A:92-111

(no "Exon" information available for 2IIF)

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:204
 aligned with IHFA_ECOLI | P0A6X7 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:204
                                                               2                                                                                                                                97  99                                  
                                                              1|          3                                                                                          95                        96| 98|                                  
                                     -         -         -    ||   -      |  6        16        26        36        46        56        66        76        86        |-         -         -    ||  99         -         -         -    
           IHFA_ECOLI     - ----------------------------------MA----------LTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENAS-------------------------PK--DE----------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee..................eeeeeeeehhhhhhhhhhhh....eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------HISTONE_LIKE        --------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iif A   1 MASTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGGSGGLTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVELSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGGSGHHHHHH 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain A from PDB  Type:PROTEIN  Length:204
 aligned with IHFB_ECOLI | P0A6Y1 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:204
                              1                                     40                                                                                                  41                                                   94         
                              |      8        18        28        38 |       -         -         -         -         -         -         -         -         -         - |      49        59        69        79        89    |    -    
           IHFB_ECOLI     - --MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQG---------------------------------------------------------------------------------------------------ERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee..................eeeeeeeehhhhhhhhhhhh....eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------HISTONE_LIKE        ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iif A   1 MASTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGGSGGLTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVELSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGGSGHHHHHH 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:DNA  Length:35
                                                                   
                 2iif C -50 CGGTGCAACAAATTGATAAGCAATGCTTTTTTGGC -16
                                   -41       -31       -21

Chain D from PDB  Type:DNA  Length:15
                                               
                 2iif D  15 GGCCAAAAAAGCATT  29
                                    24

Chain E from PDB  Type:DNA  Length:20
                                                    
                 2iif E  30 GCTTATCAATTTGTTGCACC  49
                                    39        49

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 '\|'

(no "SCOP Domain" information available for 2IIF)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IHFA_ECOLI | P0A6X7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0000746	conjugation	The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases 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:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	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.

Chain A (IHFB_ECOLI | P0A6Y1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0000746	conjugation	The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases 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:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2iif)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2iif
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IHFA_ECOLI \| P0A6X7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IHFB_ECOLI \| P0A6Y1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	IHFA_ECOLI \| P0A6X7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	IHFB_ECOLI \| P0A6Y1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	IHFA_ECOLI \| P0A6X7	:	1ihf 1ouz 1owf 1owg 2ht0 2iie 5j0n
	IHFB_ECOLI \| P0A6Y1	:	1ihf 1ouz 1owf 1owg 2ht0 2iie 5j0n

1ihf	WILD TYPE INTEGRATION HOST FACTOR-DNA COMPLEX
2iie	ENGINEERED SINGLE CHAIN INTEGRATION HOST FACTOR-DNA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 23)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File