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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR OF LACI FAMILY FROM BURKHODERIA PHYMATUM
 
Authors :  R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  05 Oct 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  11011J, Nysgxrc, Transctiptional Regulator, Laci Family, Sugar Binding Protein, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
Structural Analysis Of Transcription Regulator Of Laci Family From Burkholderia Phymatum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, LACI FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 81-359
    Gene: BPHYDRAFT_4885
    Organism Scientific: BURKHOLDERIA PHYMATUM
    Organism Taxid: 391038
    Strain: STM815

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2RGY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RGY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:292 -Pro A:293
2Ala A:311 -Pro A:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2RGY)

(-) 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:275
 aligned with B2JNW3_PARP8 | B2JNW3 from UniProtKB/TrEMBL  Length:334

    Alignment length:275
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328     
         B2JNW3_PARP8    59 LGIIGLFVPTFFGSYYGTILKQTDLELRAVHRHVVVATGCGESTPREQALEAVRFLIGRDCDGVVVISHDLHDEDLDELHRMHPKMVFLNRAFDALPDASFCPDHRRGGELAAATLIEHGHRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLIESDFSPEGGYAATCQLLESKAPFTGLFCANDTMAVSALARFQQLGISVPGDVSVIGYDDDYSAAYAAPALTSVHIPTAELTQNAVRWLINQCYGTKWEIFREFPVTVSMRASVAR 333
               SCOP domains d2rgya_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2rgyA01 A:85-187,A:319-339  [code=3.40.50.2300, no name defined]                                       2rgyA02 A:188-318,A:349-352  [code=3.40.50.2300, no name defined]                                                                  2rgyA01              ---------2rgy------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh..eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...hhhhh.eee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eeeeee............eeee.hhhhhhhhhhhhhhhhhhh...........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgy A  85 LGIIGLFVPTFFGSYYGTILKQTDLELRAVHRHVVVATGCGESTPREQALEAVRFLIGRDCDGVVVISHDLHDEDLDELHRmHPKmVFLNRAFDALPDASFCPDHRRGGELAAATLIEHGHRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLIESDFSPEGGYAATCQLLESKAPFTGLFCANDTmAVSALARFQQLGISVPGDVSVIGYDDDYSAAYAAPALTSVHIPTAELTQNAVRWLINQCYGTKWEIFREFPVTVSmRASVAR 359
                                    94       104       114       124       134       144       154       164 |   | 174       184       194       204       214       224       234       244       254       264       274  |    284       294       304       314       324       334       344       354     
                                                                                                           166-MSE                                                                                                        277-MSE                                                                     353-MSE  
                                                                                                               170-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RGY)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (B2JNW3_PARP8 | B2JNW3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008784    alanine racemase activity    Catalysis of the reaction: L-alanine = D-alanine.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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