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(-) Description

Title :  CRYSTAL STRUCTURE OF YFIR, A PUTATIVE TRANSCRIPTIONAL REGULATOR FROM BACILLUS SUBTILIS
 
Authors :  W. F. Anderson, S. S. Rajan, X. Yang, Midwest Center For Structural (Mcsg)
Date :  23 Nov 03  (Deposition) - 13 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Regulator, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Rajan, X. Yang, L. Shuvalova, F. Collart, W. F. Anderson
Crystal Structure Of Yfir, An Unusual Tetr/Camr-Type Putative Transcriptional Regulator From Bacillus Subtilis.
Proteins V. 65 255 2006
PubMed-ID: 16862575  |  Reference-DOI: 10.1002/PROT.21073

(-) Compounds

Molecule 1 - PROTEIN YFIR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMCSG7
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYFIR
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 45)

Asymmetric/Biological Unit (2, 45)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2UNX39Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:110 , UNX B:402 , UNX B:403 , UNX B:408 , UNX B:409 , UNX B:412 , UNX B:414BINDING SITE FOR RESIDUE UNX B 401
02AC2SOFTWAREILE B:172 , UNX B:401 , UNX B:408 , UNX B:409BINDING SITE FOR RESIDUE UNX B 402
03AC3SOFTWAREUNX B:401 , UNX B:408 , UNX B:412 , UNX B:414BINDING SITE FOR RESIDUE UNX B 403
04AC4SOFTWAREILE B:64 , GLY B:67 , LEU B:68 , UNX B:413 , UNX B:414BINDING SITE FOR RESIDUE UNX B 404
05AC5SOFTWAREUNX B:406 , UNX B:410 , UNX B:411 , UNX B:436BINDING SITE FOR RESIDUE UNX B 405
06AC6SOFTWAREUNX B:405 , UNX B:407 , UNX B:410 , UNX B:411 , UNX B:436BINDING SITE FOR RESIDUE UNX B 406
07AC7SOFTWAREUNX B:406 , UNX B:410 , UNX B:411 , UNX B:436BINDING SITE FOR RESIDUE UNX B 407
08AC8SOFTWAREUNX B:401 , UNX B:402 , UNX B:403 , UNX B:409 , UNX B:412 , UNX B:414BINDING SITE FOR RESIDUE UNX B 408
09AC9SOFTWAREPHE B:111 , UNX B:401 , UNX B:402 , UNX B:408 , UNX B:412BINDING SITE FOR RESIDUE UNX B 409
10BC1SOFTWAREUNX B:405 , UNX B:406 , UNX B:407 , UNX B:411 , UNX B:436BINDING SITE FOR RESIDUE UNX B 410
11BC2SOFTWAREUNX B:405 , UNX B:406 , UNX B:407 , UNX B:410 , UNX B:436BINDING SITE FOR RESIDUE UNX B 411
12BC3SOFTWAREPHE B:111 , UNX B:401 , UNX B:403 , UNX B:408 , UNX B:409 , UNX B:414BINDING SITE FOR RESIDUE UNX B 412
13BC4SOFTWAREILE B:63 , GLN B:110 , UNX B:404 , UNX B:432BINDING SITE FOR RESIDUE UNX B 413
14BC5SOFTWAREGLN B:110 , UNX B:401 , UNX B:403 , UNX B:404 , UNX B:408 , UNX B:412BINDING SITE FOR RESIDUE UNX B 414
15BC6SOFTWAREUNX A:416 , UNX A:417 , UNX A:418BINDING SITE FOR RESIDUE UNX A 415
16BC7SOFTWARELEU A:165 , UNX A:415 , UNX A:417BINDING SITE FOR RESIDUE UNX A 416
17BC8SOFTWARELEU A:127 , UNX A:415 , UNX A:416BINDING SITE FOR RESIDUE UNX A 417
18BC9SOFTWAREASP A:169 , UNX A:415 , UNX A:419 , UNX A:420BINDING SITE FOR RESIDUE UNX A 418
19CC1SOFTWAREUNX A:418 , UNX A:420 , UNX A:421 , UNX A:425BINDING SITE FOR RESIDUE UNX A 419
20CC2SOFTWAREUNX A:418 , UNX A:419 , UNX A:421 , UNX A:425BINDING SITE FOR RESIDUE UNX A 420
21CC3SOFTWAREUNX A:419 , UNX A:420 , UNX A:425BINDING SITE FOR RESIDUE UNX A 421
22CC4SOFTWAREUNX A:423 , UNX A:433 , HOH A:500 , GLN B:173 , UNX B:424 , UNX B:435BINDING SITE FOR RESIDUE UNX A 422
23CC5SOFTWAREUNX A:422 , UNX B:424 , UNX B:435BINDING SITE FOR RESIDUE UNX A 423
24CC6SOFTWAREUNX A:422 , UNX A:423 , HOH A:500 , GLN B:173 , UNX B:435BINDING SITE FOR RESIDUE UNX B 424
25CC7SOFTWAREGLN A:110 , UNX A:419 , UNX A:420 , UNX A:421BINDING SITE FOR RESIDUE UNX A 425
26CC8SOFTWAREGLY B:67 , UNX B:429BINDING SITE FOR RESIDUE UNX B 426
27CC9SOFTWARELEU A:68 , ARG A:130 , UNX A:431BINDING SITE FOR RESIDUE UNX A 427
28DC1SOFTWAREUNX A:430BINDING SITE FOR RESIDUE UNX A 428
29DC2SOFTWAREUNX B:426BINDING SITE FOR RESIDUE UNX B 429
30DC3SOFTWARETYR A:91 , UNX A:428BINDING SITE FOR RESIDUE UNX A 430
31DC4SOFTWARELEU A:68 , ARG A:130 , UNX A:427BINDING SITE FOR RESIDUE UNX A 431
32DC5SOFTWAREGLN B:110 , UNX B:413BINDING SITE FOR RESIDUE UNX B 432
33DC6SOFTWAREGLN A:173 , UNX A:422 , HOH A:500 , GLN B:173BINDING SITE FOR RESIDUE UNX A 433
34DC7SOFTWAREGLN A:173BINDING SITE FOR RESIDUE UNX A 434
35DC8SOFTWAREUNX A:422 , UNX A:423 , UNX B:424BINDING SITE FOR RESIDUE UNX B 435
36DC9SOFTWAREUNX B:405 , UNX B:406 , UNX B:407 , UNX B:410 , UNX B:411BINDING SITE FOR RESIDUE UNX B 436
37EC1SOFTWAREUNX B:438 , UNX B:439BINDING SITE FOR RESIDUE UNX B 437
38EC2SOFTWAREUNX B:437 , UNX B:439BINDING SITE FOR RESIDUE UNX B 438
39EC3SOFTWARETYR B:91 , UNX B:437 , UNX B:438BINDING SITE FOR RESIDUE UNX B 439

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.YFIR_BACSU11-71
 
  2A:11-71
B:11-71

(-) Exons   (0, 0)

(no "Exon" information available for 1RKT)

(-) 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
(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:204
 aligned with YFIR_BACSU | O31560 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           YFIR_BACSU     2 SPKVTKEHKDKRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYFSSTEEMFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNMNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK 205
               SCOP domains d1rkta1 A:2-82 Hypothetical transcriptional regulator YfiR                       d1rkta2 A:83-205 Hypothetical transcriptional regulator YfiR                                                                SCOP domains
               CATH domains 1rktA01 A:2-54 Homeodomain-like                      1rktA02 A:55-205 Tetracycline Repressor, domain 2                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------HTH_TETR_2  PDB: A:11-71 UniProt: 11-71                      -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rkt A   2 SPKVTKEHKDKRQAEILEAAKTVFKRKGFELTTmKDVVEESGFSRGGVYLYFSSTEEmFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNmNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK 205
                                    11        21        31   |    41        51       |61        71        81        91       101       111       121       131       141       151       161     | 171       181       191       201    
                                                            35-MSE                  59-MSE                                                                                                     167-MSE                                  

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with YFIR_BACSU | O31560 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
           YFIR_BACSU     6 TKEHKDKRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYFSSTEEMFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNMNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK 205
               SCOP domains d1rktb1 B:6-82 Hypothetical transcriptional regulator YfiR                   d1rktb2 B:83-205 Hypothetical transcriptional regulator YfiR                                                                SCOP domains
               CATH domains 1rktB01 B:6-54 Homeodomain-like                  1rktB02 B:55-205 Tetracycline Repressor, domain 2                                                                                                       CATH domains
           Pfam domains (1) -----------TetR_N-1rktB01 B:17-63                         ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------TetR_N-1rktB02 B:17-63                         ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: B:11-71 UniProt: 11-71                      -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkt B   6 TKEHKDKRQAEILEAAKTVFKRKGFELTTmKDVVEESGFSRGGVYLYFSSTEEmFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNmNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK 205
                                    15        25        35        45        55   |    65        75        85        95       105       115       125       135       145       155       165 |     175       185       195       205
                                                        35-MSE                  59-MSE                                                                                                     167-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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YFIR_BACSU | O31560)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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.

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