3FGH - JenaLib

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Title :   HUMAN MITOCHONDRIAL TRANSCRIPTION FACTOR A BOX B

Authors :   T. A. Gangelhoff, P. Mungalachetty, J. Nix, M. E. A. Churchill

Date :   06 Dec 08 (Deposition) - 07 Apr 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (1x)

Keywords :   Hmg Domain, Mitochondrial Transcription, Activator, Dna- Binding, Mitochondrion, Phosphoprotein, Polymorphism, Transcription, Transcription Regulation, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Gangelhoff, P. S. Mungalachetty, J. C. Nix, M. E. Churchill
Structural Analysis And Dna Binding Of The Hmg Domains Of The Human Mitochondrial Transcription Factor A
Nucleic Acids Res. V. 37 3153 2009
PubMed-ID: 19304746 | Reference-DOI: 10.1093/NAR/GKP157
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION FACTOR A, MITOCHONDRIAL
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST15
	Expression System Strain	:	BL21(DE3)+CODON
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HMG BOX 2
	Gene	:	TFAM, TCF6L2
	Organism Common	:	MAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MTTFA, MITOCHONDRIAL TRANSCRIPTION FACTOR 1, MTTF1, TRANSCRIPTION FACTOR 6-LIKE 2

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CD	2	Ligand/Ion	CADMIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:46 , GLU A:166 , HIS A:170 , CL A:178 , CL A:179	BINDING SITE FOR RESIDUE CD A 1
2	AC2	SOFTWARE	HOH A:28 , HOH A:34 , ASP A:152 , GLU A:164	BINDING SITE FOR RESIDUE CD A 2
3	AC3	SOFTWARE	CD A:1 , HOH A:46 , ALA A:119 , GLU A:166 , HIS A:170	BINDING SITE FOR RESIDUE CL A 178
4	AC4	SOFTWARE	CD A:1 , HOH A:46 , ARG A:115 , GLU A:166 , TYR A:169	BINDING SITE FOR RESIDUE CL A 179
5	AC5	SOFTWARE	HOH A:52 , HOH A:53 , ASP A:165	BINDING SITE FOR RESIDUE NA A 180
6	AC6	SOFTWARE	SER A:151 , SER A:153	BINDING SITE FOR RESIDUE NA A 181

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

Asymmetric Unit

No.	Residues
1	Lys A:132	-	Gly A:133

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_077842	P	178	L	TFAM_HUMAN	Disease (MTDPS15)	757075712	A	P	136	L

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_077842	P	178	L	TFAM_HUMAN	Disease (MTDPS15)	757075712	A	P	136	L

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_077842	P	178	L	TFAM_HUMAN	Disease (MTDPS15)	757075712	A	P	136	L

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	TFAM_HUMAN	50-118 155-219	1	- A:113-176

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	TFAM_HUMAN	50-118 155-219	2	- A:113-176

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	TFAM_HUMAN	50-118 155-219	1	- A:113-176

(no "Exon" information available for 3FGH)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:67
 aligned with TFAM_HUMAN | Q00059 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:67
                                   162       172       182       192       202       212       
           TFAM_HUMAN   153 GKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWE 219
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains 3fghA00 A:111-177 DNA Binding (I), subunit A                        CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------L----------------------------------------- SAPs(SNPs)
                    PROSITE --HMG_BOX_2  PDB: A:113-176 UniProt: 155-219                        PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 3fgh A 111 GKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWA 177
                                   120       130       140       150       160       170

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 3FGH)

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA Binding (I), subunit A (33)

Homologous Superfamily: DNA Binding (I), subunit A (33)

Man (Homo sapiens) (1)

3fghA00

A:111-177

(no "Pfam Domain" information available for 3FGH)

Asymmetric Unit(hide GO term definitions)

Chain A (TFAM_HUMAN | Q00059)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008301	DNA binding, bending	The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0031072	heat shock protein binding	Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
	GO:0070363	mitochondrial light strand promoter sense binding	Interacting selectively and non-covalently with the sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0001223	transcription coactivator binding	Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	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.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	GO:0033108	mitochondrial respiratory chain complex assembly	The aggregation, arrangement and bonding together of a set of components to form a mitochondrial respiratory chain complex.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0006356	regulation of transcription from RNA polymerase I promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006390	transcription from mitochondrial promoter	The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.
	GO:0006391	transcription initiation from mitochondrial promoter	A transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0042645	mitochondrial nucleoid	The region of a mitochondrion to which the DNA is confined.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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		Lys A:132 - Gly A:133	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

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