1PDN | PDR018 - JenaLib

Title :   CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS

Authors :   W. Xu, M. A. Rould, S. Jun, C. Desplan, C. O. Pabo

Date :   16 May 95 (Deposition) - 31 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Protein-Dna Complex, Double Helix, Pax, Prd, Paired Domain, Dna-Binding Protein, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Xu, M. A. Rould, S. Jun, C. Desplan, C. O. Pabo
Crystal Structure Of A Paired Domain-Dna Complex At 2. 5 A Resolution Reveals Structural Basis For Pax Developmental Mutations.
Cell(Cambridge, Mass. ) V. 80 639 1995
PubMed-ID: 7867071 | Reference-DOI: 10.1016/0092-8674(95)90518-9
(for further references see the PDB file header)

Compounds

*Molecule 1 - DNA (5'- D(APAPCPGPTPCPAPCPGPGPTPTPGPAPC)-3')**
	Chains	:	A
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(TPTPGPTPCPAPAPCPCPGPTPGPAPCPG)-3')**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN (PRD PAIRED)
	Chains	:	C
	Engineered	:	YES
	Expression System	:	BL21(DE3)
	Expression System Common	:	BL21(DE3)
	Expression System Gene	:	PRD
	Expression System Plasmid	:	PET14BPRDPDB
	Gene	:	PRD
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:DNA  Length:15
                                               
                 1pdn A   1 AACGTCACGGTTGAC  15
                                    10

Chain B from PDB  Type:DNA  Length:15
                                               
                 1pdn B  16 TTGTCAACCGTGACG  30
                                    25

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with PRD_DROME | P06601 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:123
                                    37        47        57        67        77        87        97       107       117       127       137       147   
            PRD_DROME    28 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV 150
               SCOP domains d1pdnc1 C:2-66 Paired protein (prd)                              d1pdnc2 C:67-124 Paired protein (prd)                      SCOP domains
               CATH domains 1pdnC01 C:2-69 'winged helix' repressor DNA binding domain          1pdnC02 C:70-124                                        CATH domains
               Pfam domains PAX-1pdnC01 C:2-124                                                                                                         Pfam domains
         Sec.struct. author .eee.....eee......hhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhh...................hhhhhhh.........hhhhhhhhhh...........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PAIRED_1         ------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdn C   2 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

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Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C (PRD_DROME | P06601)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	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.
	GO:0003705	transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
biological process
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007366	periodic partitioning by pair rule gene	Allocation of cells to parasegments in the embryo, through the action of overlapping series of pair rule gene activities.
	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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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