1LB2 | PD0306 - JenaLib

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Title :   STRUCTURE OF THE E. COLI ALPHA C-TERMINAL DOMAIN OF RNA POLYMERASE IN COMPLEX WITH CAP AND DNA

Authors :   B. Benoff, H. Yang, C. L. Lawson, G. Parkinson, J. Liu, E. Blatter, Y. W. Ebright, H. M. Berman, R. H. Ebright

Date :   01 Apr 02 (Deposition) - 06 Sep 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B,E,J,K
Biol. Unit 1: A,B,E,J,K  (2x)

Keywords :   Protein-Dna Complex, Gene-Regulatory, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Benoff, H. Yang, C. L. Lawson, G. Parkinson, J. Liu, E. Blatter, Y. W. Ebright, H. M. Berman, R. H. Ebright
Structural Basis Of Transcription Activation: The Cap-Alpha Ctd-Dna Complex.
Science V. 297 1562 2002
PubMed-ID: 12202833 | Reference-DOI: 10.1126/SCIENCE.1076376
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPTPTPTPTPTPTPCPCPTPAPAPAPAPTPGPTPGPAP T)-3'*
	Chains	:	K
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPTPAPGPAPTPCPAPCPAPTPTPTPTPAPGPGPAPAP APAPAPAPG)-3'*
	Chains	:	J
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - CATABOLITE GENE ACTIVATOR PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CAP, CAMP RECEPTOR PROTEIN, CAMP-REGULATORY PROTEIN

Molecule 4 - DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN
	Chains	:	B, E
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ALPHA CTD, ALPHA CARBOXY TERMINAL DOMAIN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRANSCRIPTASE ALPHA CHAIN, RNA POLYMERASE ALPHA SUBUNIT

		1	2	3	4	5
Asymmetric Unit	:	A	B	E	J	K
Biological Unit 1 (2x)	:	A	B	E	J	K

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CMP	1	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CMP	2	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:30 , VAL A:49 , LEU A:61 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , TYR A:99 , THR A:127 , SER A:128	BINDING SITE FOR RESIDUE CMP A 679

(no "SS Bond" information available for 1LB2)

(no "Cis Peptide Bond" information available for 1LB2)

(no "SAP(SNP)/Variant" information available for 1LB2)

Asymmetric Unit (5, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRP_ECOLI	24-124	1	A:23-123
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CRP_ECOLI	30-46	1	A:29-45
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CRP_ECOLI	71-89	1	A:70-88
4	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRP_ECOLI	138-210	1	A:137-209
5	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CRP_ECOLI	168-191	1	A:167-190

Biological Unit 1 (5, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRP_ECOLI	24-124	2	A:23-123
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CRP_ECOLI	30-46	2	A:29-45
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CRP_ECOLI	71-89	2	A:70-88
4	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRP_ECOLI	138-210	2	A:137-209
5	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CRP_ECOLI	168-191	2	A:167-190

(no "Exon" information available for 1LB2)

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:201
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:201
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
            CRP_ECOLI    10 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d1lb2a2 A:9-137 Catabolite gene activator protein, N-terminal domain                                                             d1lb2a1 A:138-209                                                        SCOP domains
               CATH domains 1lb2A01 A:9-137 Jelly Rolls                                                                                                      1lb2A02 A:138-206 'winged helix' repressor DNA binding domain        --- CATH domains
               Pfam domains -----------cNMP_binding-1lb2A02 A:20-111                                                               -----------------------------------------------------Crp-1lb2A01 A:165-196           ------------- Pfam domains
         Sec.struct. author hhhhhhhh..eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhh........eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: A:137-209 UniProt: 138-210                                PROSITE (1)
                PROSITE (2) --------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lb2 A   9 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:72
                                   259       269       279       289       299       309       319  
           RPOA_ECOLI   250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 321
               SCOP domains d1lb2b_ B: C-terminal domain of RNA polymerase alpha subunit             SCOP domains
               CATH domains 1lb2B00 B:250-321 5' to 3' exonuclease, C-terminal subdomain             CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhhhh...hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1lb2 B 250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 321
                                   259       269       279       289       299       309       319

Chain E from PDB  Type:PROTEIN  Length:66
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:66
                                   259       269       279       289       299       309      
           RPOA_ECOLI   250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 315
               SCOP domains d1lb2e_ E: C-terminal domain of RNA polymerase alpha subunit       SCOP domains
               CATH domains 1lb2E00 E:250-315 5' to 3' exonuclease, C-terminal subdomain       CATH domains
           Pfam domains (1) RNA_pol_A_CTD-1lb2E01 E:250-309                             ------ Pfam domains (1)
           Pfam domains (2) RNA_pol_A_CTD-1lb2E02 E:250-309                             ------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhh....hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1lb2 E 250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 315
                                   259       269       279       289       299       309

Chain J from PDB  Type:DNA  Length:24
                                                        
                 1lb2 J  10 CTAGATCACATTTTAGGAAAAAAG  33
                                    19        29

Chain K from PDB  Type:DNA  Length:20
                                                    
                 1lb2 K  33 CTTTTTTCCTAAAATGTGAT  14
                            ||||||||24||||||||14
                           33|||||||24|||||||15|
                            32|||||||23|||||||14
                             31|||||| 22||||||  
                              30|||||  21|||||  
                               29||||   20||||  
                                28|||    19|||  
                                 27||     18||  
                                  26|      17|  
                                   25       16

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1lb2A02

A:138-206

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: 5' to 3' exonuclease, C-terminal subdomain (384)

[unclassified] (230)

2a	1lb2B00	B:250-321
2b	1lb2E00	E:250-315

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

[unclassified] (14)

1lb2A01

A:9-137

Asymmetric Unit(hide GO term definitions)

Chain A (CRP_ECOLI | P0ACJ8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	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.
	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: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:0045013	carbon catabolite repression of transcription	A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
	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: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: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.

Chain B,E (RPOA_ECOLI | P0A7Z4)

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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1lb2)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1lb2
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(no "Related Entries Specified in the PDB File" available for 1LB2)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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