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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A PURR FAMILY TRANSCRIPTIONAL REGULATOR FROM VIBRIO PARAHAEMOLYTICUS RIMD 2210633
 
Authors :  K. Tan, C. Hatzos, S. Moy, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  23 May 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apc91343. 1, Purr, Transcriptional Regulator, Vibrio Parahaemolyticus Rimd 2210633, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna- Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Hatzos, S. Moy, A. Joachimiak
The Crystal Structure Of A Purr Family Transcriptional Regulator From Vibrio Parahaemolyticus Rimd 2210633
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PURR TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG8
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Gene: VPA0232
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670
    Strain: RIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

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

(-) Sites  (0, 0)

(no "Site" information available for 3D8U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D8U)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:274 -Pro A:275
2Tyr A:293 -Pro A:294
3Val B:274 -Pro B:275
4Tyr B:293 -Pro B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D8U)

(-) Exons   (0, 0)

(no "Exon" information available for 3D8U)

(-) 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:264
 aligned with Q87JL7_VIBPA | Q87JL7 from UniProtKB/TrEMBL  Length:342

    Alignment length:270
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
         Q87JL7_VIBPA    71 YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 340
               SCOP domains d3d8ua_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3d8uA01 A:71-167,A:302-321  [code=3.40.50.2300, no name defined]                                 3d8uA02 A:168-301,A:328-340  [code=3.40.50.2300, no name defined]                                                                     3d8uA01             ------3d8uA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..ee..ee...hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeee.........eee..hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeee...hhhhhh.....eeee.hhhhhhhhhhhhhhhhhh..------....eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d8u A  71 YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAmIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSmGEHAYPSLTSAEFDYERmGTKAAEKLLHAIKGE------SmGFKLKRRASTA 340
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210  |    220       230       240       250       260       270       280       290       300     | 310       320|      330       340
                                                                                                                                                                        213-MSE                                                                    288-MSE           306-MSE        321    328|           
                                                                                                                                                                                                                                                                                            329-MSE       


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with Q87JL7_VIBPA | Q87JL7 from UniProtKB/TrEMBL  Length:342

    Alignment length:272
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
         Q87JL7_VIBPA    71 YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 342
               SCOP domains d3d8ub_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3d8uB01 B:71-167,B:302-326  [code=3.40.50.2300, no name defined]                                 3d8uB02 B:168-301,B:327-342  [code=3.40.50.2300, no name defined]                                                                     3d8uB01                  3d8uB02          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh...eeee.........eee..hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eeee...hhhhhh......eee.hhhhhhhhhhhhhhhhhh-....-......eee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8u B  71 YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAmIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSmGEHAYPSLTSAEFDYERmGTKAAEKLLHAIK-EPEE-PTSmGFKLKRRASTAIN 342
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210  |    220       230       240       250       260       270       280       290       300     | 310        |-|  | | 330       340  
                                                                                                                                                                        213-MSE                                                                    288-MSE           306-MSE      319 |  | |  |             
                                                                                                                                                                                                                                                                                    321  | |  |             
                                                                                                                                                                                                                                                                                       324 |  |             
                                                                                                                                                                                                                                                                                         326  |             
                                                                                                                                                                                                                                                                                            329-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  (1, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D8U)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87JL7_VIBPA | Q87JL7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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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  Cis Peptide Bonds
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    Val A:274 - Pro A:275   [ RasMol ]  
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