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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR PF0095 FROM PYROCOCCUS FURIOSUS
 
Authors :  H. Yang, G. L. Lipscomb, R. A. Scott, J. P. Rose, B. C. Wang
Date :  13 Jul 07  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yang, G. L. Lipscomb, R. A. Scott, J. P. Rose, B. C. Wang
Crystal Structure Of Transcription Factor Pf0095 From Pyrococcus Furiosus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR PF0095
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21-CODONPLUS (DE3)-RIPL
    Expression System Vector Type: PLASMID
    Organism Common: ARCHAEA
    Organism Scientific: PYROCOCCUS FURIOSUS
    Other Details: SEMET LABELED

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 30)

Asymmetric Unit (1, 30)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QLZ)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:26
2B:23 -B:26
3C:23 -C:26
4D:23 -D:26

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:39 -Thr B:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QLZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QLZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2QLZ)

(-) 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:219
 aligned with Q8U4J2_PYRFU | Q8U4J2 from UniProtKB/TrEMBL  Length:232

    Alignment length:224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
         Q8U4J2_PYRFU     2 EPDLFYILGNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISIAKSYVFTLTPEMFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEMITDFIKANKELEKVLEAFKTIESYRSSLMRKIKEAYLKEIGDMTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEMARFVPVKIINDNTVVLDEDQILR 225
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh..eeeeee..-----.eeeeee...eeeeeeee..eeeeeeee........eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhh....eeee...eeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qlz A   2 EPDLFYILGNKVRRDLLSHLTCmECYFSLLSSKVSVSSTAVAKHLKImEREGVLQSYEKEE-----TKKYYKISIAKSYVFTLTPEmFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEmITDFIKANKELEKVLEAFKTIESYRSSLmRKIKEAYLKEIGDmTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEmARFVPVKIINDNTVVLDEDQILR 225
                                    11        21  |     31        41       |51        61|     | 71        81      | 91       101       111       121       131       141       151       161  |    171       181       191       201|      211       221    
                                                 24-MSE                   49-MSE       62    68                  88-MSE                          121-MSE                      150-MSE       164-MSE                               202-MSE                   


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q8U4J2_PYRFU | Q8U4J2 from UniProtKB/TrEMBL  Length:232

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
         Q8U4J2_PYRFU     1 MEPDLFYILGNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISIAKSYVFTLTPEMFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEMITDFIKANKELEKVLEAFKTIESYRSSLMRKIKEAYLKEIGDMTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEMARFVPVKIINDNTVVLDEDQILR 225
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh..eeeee.....----.eeeee...eeeeeee....eeeeeee...-...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeehhhhhhhhh.hhhhhhhhhhhhh....eeee...eeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qlz B   1 mEPDLFYILGNKVRRDLLSHLTCmECYFSLLSSKVSVSSTAVAKHLKImEREGVLQSYEKEERF----KKYYKISIAKSYVFTLTPEmFWYKGLDLGD-ELRDFEISLSGLDTEPSTLKEmITDFIKANKELEKVLEAFKTIESYRSSLmRKIKEAYLKEIGDmTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEmARFVPVKIINDNTVVLDEDQILR 225
                            |       10        20   |    30        40        50        60   |    70        80       |90       100       110       120|      130       140       150       160   |   170       180       190       200 |     210       220     
                            1-MSE                 24-MSE                   49-MSE         64   69                 88-MSE    98 |                  121-MSE                      150-MSE       164-MSE                               202-MSE                   
                                                                                                                             100                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with Q8U4J2_PYRFU | Q8U4J2 from UniProtKB/TrEMBL  Length:232

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
         Q8U4J2_PYRFU     2 EPDLFYILGNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISIAKSYVFTLTPEMFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEMITDFIKANKELEKVLEAFKTIESYRSSLMRKIKEAYLKEIGDMTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEMARFVPVKIINDNTVVLDEDQI 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.......-..hhhhhhhhhhhhhhh..eeeee.-------..eeeee...eeeeeee....eeeeeee...-....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhh....eeee...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qlz C   2 EPDLFYILGNKVRRDLLSHLTCmECYFSLLSSK-SVSSTAVAKHLKImEREGVLQSYEK-------TKKYYKISIAKSYVFTLTPEmFWYKGLDLGD-ELRDFEISLSGLDTEPSTLKEmITDFIKANKELEKVLEAFKTIESYRSSLmRKIKEAYLKEIGDmTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEmARFVPVKIINDNTVVLDEDQI 223
                                    11        21  |     31  | |   41       |51        |-      | 71        81      | 91      |101       111       121       131       141       151       161  |    171       181       191       201|      211       221  
                                                 24-MSE    34 |           49-MSE     60      68                  88-MSE    98 |                  121-MSE                      150-MSE       164-MSE                               202-MSE                 
                                                             36                                                             100                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with Q8U4J2_PYRFU | Q8U4J2 from UniProtKB/TrEMBL  Length:232

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
         Q8U4J2_PYRFU     1 MEPDLFYILGNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISIAKSYVFTLTPEMFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEMITDFIKANKELEKVLEAFKTIESYRSSLMRKIKEAYLKEIGDMTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEMARFVPVKIINDNTVVLDEDQILR 225
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --HTH_20-2qlzD01 D:3-59                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --HTH_20-2qlzD02 D:3-59                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --HTH_20-2qlzD03 D:3-59                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --HTH_20-2qlzD04 D:3-59                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhh..eeee.---------..eeee...eeeeeeee..eeeeeeee.......eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeehhhhhhhhh.hhhhhhhhhhhhh....eeee...eeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qlz D   1 mEPDLFYILGNKVRRDLLSHLTCmECYFSLLSSKVSVSSTAVAKHLKImEREGVLQSYE---------KKYYKISIAKSYVFTLTPEmFWYKGLDLGDAELRDFEISLSGLDTEPSTLKEmITDFIKANKELEKVLEAFKTIESYRSSLmRKIKEAYLKEIGDmTQLAILHYLLLNGRATVEELSDRLNLKEREVREKISEmARFVPVKIINDNTVVLDEDQILR 225
                            |       10        20   |    30        40        50        |-        70        80       |90       100       110       120|      130       140       150       160   |   170       180       190       200 |     210       220     
                            1-MSE                 24-MSE                   49-MSE    59        69                 88-MSE                          121-MSE                      150-MSE       164-MSE                               202-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2QLZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QLZ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8U4J2_PYRFU | Q8U4J2)
molecular function
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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 Related Entries

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UniProtKB/TrEMBL
        Q8U4J2_PYRFU | Q8U4J2: 2quf

(-) Related Entries Specified in the PDB File

2quf MUTANT PROTEIN, C23A, C26A