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(-) Description

Title :  E. COLI RNA POLYMERASE ALPHA SUBUNIT C-TERMINAL DOMAIN IN COMPLEX WITH CAP AND DNA
 
Authors :  S. Lara-Gonzalez, J. J. Birktoft, C. L. Lawson
Date :  21 May 10  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Protein-Protein Interactions, Protein-Dna Interactions, Gene Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lara-Gonzalez, J. J. Birktoft, C. L. Lawson
Combined Structural Model For A Transcription Activation Assembly
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATABOLITE GENE ACTIVATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B3357, CAP, CRP, CSM, JW5702
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CAMP RECEPTOR PROTEIN, CAMP REGULATORY PROTEIN
 
Molecule 2 - DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA
    Chains: B, C
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALPHA SUBUNIT C-TERMINAL DOMAIN, RESIDUES 246-329
    Gene: B3295, JW3257, PEZ, PHS, RPOA, SEZ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: RNAP SUBUNIT ALPHA, TRANSCRIPTASE SUBUNIT ALPHA, RNA POLYMERASE SUBUNIT ALPHA
 
Molecule 3 - DNA (5'- D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP* AP*G)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:49 , LEU A:61 , GLY A:71 , GLU A:72 , LEU A:73 , GLY A:74 , ARG A:82 , SER A:83 , ALA A:84 , ARG A:123 , LEU A:124 , THR A:127 , SER A:128BINDING SITE FOR RESIDUE CMP A 210
2AC2SOFTWARETHR A:10 , ASN A:109BINDING SITE FOR RESIDUE PEG A 501
3AC3SOFTWAREASP A:161BINDING SITE FOR RESIDUE PEG A 502
4AC4SOFTWAREDT D:17 , DC E:27 , DA E:28BINDING SITE FOR RESIDUE CMP D 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N4M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp B:321 -Pro B:322
2Trp C:321 -Pro C:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N4M)

(-) PROSITE Motifs  (5, 5)

Asymmetric Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRP_ECOLI24-124  1A:23-123
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CRP_ECOLI30-46  1A:29-45
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CRP_ECOLI71-89  1A:70-88
4HTH_CRP_2PS51063 Crp-type HTH domain profile.CRP_ECOLI138-210  1A:137-209
5HTH_CRP_1PS00042 Crp-type HTH domain signature.CRP_ECOLI168-191  1A:167-190
Biological Unit 1 (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRP_ECOLI24-124  2A:23-123
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CRP_ECOLI30-46  2A:29-45
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CRP_ECOLI71-89  2A:70-88
4HTH_CRP_2PS51063 Crp-type HTH domain profile.CRP_ECOLI138-210  2A:137-209
5HTH_CRP_1PS00042 Crp-type HTH domain signature.CRP_ECOLI168-191  2A:167-190

(-) Exons   (0, 0)

(no "Exon" information available for 3N4M)

(-) Sequences/Alignments

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:203
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
            CRP_ECOLI     8 TDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d3n4ma1 A:7-137 Catabolite gene activator protein, N-terminal domain                                                               d3n4ma2 A:138-209                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------cNMP_binding-3n4mA02 A:20-111                                                               -----------------------------------------------------Crp-3n4mA01 A:165-196           ------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee.hhhhh........eeee...eeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........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
                 3n4m A   7 TDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:74
                                   258       268       278       288       298       308       318    
           RPOA_ECOLI   249 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP 322
               SCOP domains d3n4mb_ B: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 3n4m B 249 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP 322
                                   258       268       278       288       298       308       318    


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:73
                                   259       269       279       289       299       309       319   
           RPOA_ECOLI   250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP 322
               SCOP domains d3n4mc_ C: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RNA_pol_A_CTD-3n4mC01 C:250-309                             ------------- Pfam domains (1)
           Pfam domains (2) RNA_pol_A_CTD-3n4mC02 C:250-309                             ------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3n4m C 250 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWP 322
                                   259       269       279       289       299       309       319   


Chain D from PDB  Type:DNA  Length:20
                                                    
                 3n4m D   1 CTTTTTTCCTAAAATGTGAT  20
                                    10        20


Chain E from PDB  Type:DNA  Length:24
                                                        
                 3n4m E  21 CTAGATCACATTTTAGGAAAAAAG  44
                                    30        40
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N4M)

(-) Pfam Domains  (3, 4)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: RNA_pol_A_CTD] (7)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (19, 23)

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,C   (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.

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  3n4m
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CRP_ECOLI | P0ACJ8: 1cgp 1g6n 1hw5 1i5z 1i6x 1j59 1lb2 1o3q 1o3r 1o3s 1o3t 1run 1ruo 1zrc 1zrd 1zre 1zrf 2cgp 2gap 2gzw 2wc2 3fwe 3hif 3iyd 3kcc 3qop 3rdi 3rou 3rpq 3ryp 3ryr 4bh9 4bhp 4ft8 4hzf 4i01 4i02 4i09 4i0a 4i0b 4r8h 5ciz
        RPOA_ECOLI | P0A7Z4: 1bdf 1coo 1lb2 1xs9 2jzb 3iyd 3k4g 3lu0 3n97 4jk1 4jk2 4kmu 4kn4 4kn7 4mex 4mey 4s20 4xsx 4xsy 4xsz 4yg2 4yln 4ylo 4ylp 4zh2 4zh3 4zh4 5byh 5ciz 5ezk 5ipl 5ipm 5ipn 5ms0 5my1 5nsr 5nss 5uac 5uag 5uah 5uaj 5ual 5uaq 5up6 5upc 5vsw 5w1s 5w1t

(-) Related Entries Specified in the PDB File

1lb2 THIS ENTRY IS A RE-DETERMINATION OF THE 1LB2 CAP-ALPHA CTD- DNA COMPLEX USING NEW DIFFRACTION DATA
3k4g CRYSTAL STRUCTURE OF E. COLI RNA POLYMERASE ALPHA SUBUNIT C -TERMINAL DOMAIN
3n97 RNA POLYMERASE ALPHA C-TERMINAL DOMAIN (E. COLI) AND SIGMA REGION 4 (T. AQ. MUTANT) BOUND TO (UP,-35 ELEMENT) DNA