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Title :   STRUCTURE OF AN ARCHEAL HOMOLOG OF THE EUKARYOTIC RNA POLYMERASE II RPB4/RPB7 COMPLEX

Authors :   F. Todone, P. Brick, F. Werner, R. O. J. Weinzierl, S. Onesti

Date :   17 Oct 01 (Deposition) - 07 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : E,F,M,N
Biol. Unit 1: E,F  (1x)
Biol. Unit 2: M,N  (1x)

Keywords :   Transferase, Transferase; Transcription; Dna-Directed Rna Polymerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Todone, P. Brick, F. Werner, R. O. J. Weinzierl, S. Onesti
Structure Of An Archaeal Homolog Of The Eukaryotic Rna Polymerase Ii Rpb4/Rpb7 Complex
Mol. Cell V. 8 1137 2001
PubMed-ID: 11741548 | Reference-DOI: 10.1016/S1097-2765(01)00379-3

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT E
	Chains	:	E, M
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2TK
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	DE3
	Organism Scientific	:	METHANOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Other Details	:	CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY

Molecule 2 - DNA-DIRECTED RNA POLYMERASE SUBUNIT F
	Chains	:	F, N
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2TX
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	DE3
	Organism Scientific	:	METHANOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Other Details	:	CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY

		1	2	3	4
Asymmetric Unit	:	E	F	M	N
Biological Unit 1 (1x)	:	E	F
Biological Unit 2 (1x)	:			M	N

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1GO3)

(no "Site" information available for 1GO3)

(no "SS Bond" information available for 1GO3)

(no "Cis Peptide Bond" information available for 1GO3)

(no "SAP(SNP)/Variant" information available for 1GO3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	RPOE1_METJA	82-166	2	E:82-166 M:82-166

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	RPOE1_METJA	82-166	1	E:82-166 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	RPOE1_METJA	82-166	1	- M:82-166

(no "Exon" information available for 1GO3)

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 E from PDB  Type:PROTEIN  Length:177
 aligned with RPOE1_METJA | Q57840 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
          RPOE1_METJA     1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEKAKKQ 184
               SCOP domains d1go3e2 E:1-78 N-terminal, heterodimerisation domain of RBP7 (RpoE)           d1go3e1 E:79-184 C-terminal domain of RNA pol  ymerase II subunit RBP7 (Rpo     E)                         SCOP domains
               CATH domains 1go3E02 E:1-81 DNA-directed RNA polymerase ii subunit; domain 1                  1go3E01 E:82-182 Nucleic acid-binding prot  eins                                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeehhhhh..hhhhhhhhhhhhhhh..ee...eeeeeeeeeeee...........eeeeeeeeeeee......eeeeeeeeee..eeeee....eeeee.hhh....eee...--.eee.....ee....eeeeeeeeee...-----.eeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------S1  PDB: E:82-166 UniProt: 82-166                                                    ------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1go3 E   1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPK--AIIGKETGKVLEIGDYVRARIVAISLKA-----SKIALTMRQPYLGKLEWIEEEKAKKQ 184
                                    10        20        30        40        50        60        70        80        90       100       110       120  |  | 130       140       150  |    160       170       180    
                                                                                                                                                    123  |                        153   159                         
                                                                                                                                                       126

Chain F from PDB  Type:PROTEIN  Length:107
 aligned with Y039_METJA | Q60351 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:107
                                    18        28        38        48        58        68        78        88        98       108       
           Y039_METJA     9 MIGKKILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKLDKEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRKYI 115
               SCOP domains d1go3f_ F: RNA polymerase II subunit RBP4 (RpoF)                                                            SCOP domains
               CATH domains 1go3F02 F:1-47                                 1go3F01 F:48-107  [code=1.10.150.80, no name defined]        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1go3 F   1 MIGKKILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKLDKEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRKYI 107
                                    10        20        30        40        50        60        70        80        90       100

Chain M from PDB  Type:PROTEIN  Length:174
 aligned with RPOE1_METJA | Q57840 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
          RPOE1_METJA     1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEKA 181
               SCOP domains d1go3m2 M:1-78 N-terminal, heterodimerisation domain of RBP7 (RpoE)           d1go3m1 M:79-181 C-terminal domain of RNA polymerase II subunit RBP7 (Rpo       E)                      SCOP domains
               CATH domains 1go3M02 M:1-81 DNA-directed RNA polymerase ii subunit; domain 1                  1go3M01 M:82-180 Nucleic acid-binding proteins                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeehhhhh..hhhhhhhhhhhhhhh..ee...eeeeeeeeeeee...........eeeeeeeeeeee......eeeeeeeeee..eeeee....eeeee.hhh....eeee....eeee.....eee...eeeeeeeeee.-------.eeeee........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------S1  PDB: M:82-166 UniProt: 82-166                                                    --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1go3 M   1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISL-------SKIALTMRQPYLGKLEWIEEEKA 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      160       170       180 
                                                                                                                                                                                151     159

Chain N from PDB  Type:PROTEIN  Length:106
 aligned with Y039_METJA | Q60351 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:106
                                    19        29        39        49        59        69        79        89        99       109      
           Y039_METJA    10 IGKKILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKLDKEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRKYI 115
               SCOP domains d1go3n_ N: RNA polymerase II subunit RBP4 (RpoF)                                                           SCOP domains
               CATH domains 1go3N02 N:2-47                                1go3N01 N:48-107  [code=1.10.150.80, no name defined]        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1go3 N   2 IGKKILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKLDKEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRKYI 107
                                    11        21        31        41        51        61        71        81        91       101

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 "Pfam Domain" information available for 1GO3)

Asymmetric Unit(hide GO term definitions)

Chain E,M (RPOE1_METJA | Q57840)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000428	DNA-directed RNA polymerase complex	A protein complex that possesses DNA-directed RNA polymerase activity.

Chain F,N (Y039_METJA | Q60351)

molecular function
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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Biological Units
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		Biological Unit 2	[ Jena3D ]

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	RPOE1_METJA \| Q57840
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	Y039_METJA \| Q60351
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(no "Entries Sharing at Least One Protein Chain" available for 1GO3)

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Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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