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(-) Description

Title :  CRYSTAL STRUCTURE OF PERIPLASMIC BINDING PROTEIN/LACI TRANSCRIPTIONAL REGULATOR FROM ALKALIPHILUS METALLIREDIGENS QYMF COMPLEXED WITH D-XYLULOFURANOSE
 
Authors :  V. N. Malashkevich, R. Toro, S. R. Wasserman, A. Meyer, J. M. Sauder, S. K S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)
Date :  14 Apr 08  (Deposition) - 06 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transcriptional Regulator, L-Xylulose, D-Xylulofuranose, Dna-Binding, Transcription Regulation, Transcription Regulator, Psi-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. N. Malashkevich, R. Toro, S. R. Wasserman, A. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Periplasmic Binding Protein/Laci Transcriptional Regulator From Alkaliphilus Metalliredigens Qymf Complexed With L-Xylulose.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PERIPLASMIC BINDING PROTEIN/LACI TRANSCRIPTIONAL REGULATOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBC-PSGX3(BC)
    Expression System StrainBL21(DE3)CODON+RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAMET_0586
    Organism ScientificALKALIPHILUS METALLIREDIGENS
    Organism Taxid293826
    StrainQYMF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2XLF2Ligand/IonBETA-D-XYLULOFURANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:72 , PHE A:74 , ARG A:124 , GLU A:142 , THR A:187 , ARG A:190 , ASN A:239 , ASP A:267 , GLN A:284BINDING SITE FOR RESIDUE XLF A 401
2AC2SOFTWAREASN B:72 , PHE B:74 , ARG B:124 , GLU B:142 , THR B:187 , ARG B:190 , ASN B:239 , ASP B:267 , GLN B:284BINDING SITE FOR RESIDUE XLF B 401
3AC3SOFTWAREVAL A:230 , TYR A:232 , GLU A:260 , HOH A:544 , HOH A:586BINDING SITE FOR RESIDUE NA A 402
4AC4SOFTWAREVAL B:230 , TYR B:232 , GLU B:260 , HOH B:708 , HOH B:764BINDING SITE FOR RESIDUE NA B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:257 -Pro A:258
2Tyr A:276 -Pro A:277
3Ile B:257 -Pro B:258
4Tyr B:276 -Pro B:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CTP)

(-) 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:266
 aligned with A6TKU5_ALKMQ | A6TKU5 from UniProtKB/TrEMBL  Length:333

    Alignment length:266
                                    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      
         A6TKU5_ALKMQ    59 SKTIGLMVPNISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQCEDEYANIDIPVVAFENHILDNIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFIEFQHDFQVKMLEEDINSMKDIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGFDNSFIGELLYPSLTTINQPIEALAYTIIELLIKIINGEGVLIEDYIMEVKLIERETTIS 324
               SCOP domains d3ctpa_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3ctpA01 A:60-155,A:284-315  [code=3.40.50.2300, no name defined]                                3ctpA02 A:156-283,A:316-325  [code=3.40.50.2300, no name defined]                                                               3ctpA01 A:60-155,A:284-315      3ctpA02    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhh.....eeee.........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhh...hhhhhhhh.eeee.hhhhhhhhhhhhhhh........eee.....hhhhhh.....eee.hhhhhhhhhhhhhhhhhhh.......eee..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ctp A  60 SKTIGLMVPNISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQCEDEYANIDIPVVAFENHILDNIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFIEFQHDFQVKMLEEDINSMKDIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGFDNSFIGELLYPSLTTINQPIEALAYTIIELLIKIINGEGVLIEDYIMEVKLIERETTIS 325
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319      

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with A6TKU5_ALKMQ | A6TKU5 from UniProtKB/TrEMBL  Length:333

    Alignment length:266
                                    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      
         A6TKU5_ALKMQ    59 SKTIGLMVPNISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQCEDEYANIDIPVVAFENHILDNIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFIEFQHDFQVKMLEEDINSMKDIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGFDNSFIGELLYPSLTTINQPIEALAYTIIELLIKIINGEGVLIEDYIMEVKLIERETTIS 324
               SCOP domains d3ctpb_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3ctpB01 B:60-155,B:284-315  [code=3.40.50.2300, no name defined]                                3ctpB02 B:156-283,B:316-325  [code=3.40.50.2300, no name defined]                                                               3ctpB01 B:60-155,B:284-315      3ctpB02    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhh.....eeee.........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh....eeee.....hhhhhhh...hhhhhhhh.eeee.hhhhhhhhhhhhhhh........eee.....hhhhhh.....eee.hhhhhhhhhhhhhhhhhhh.......eee..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ctp B  60 SKTIGLMVPNISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQCEDEYANIDIPVVAFENHILDNIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFIEFQHDFQVKMLEEDINSMKDIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGFDNSFIGELLYPSLTTINQPIEALAYTIIELLIKIINGEGVLIEDYIMEVKLIERETTIS 325
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319      

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6TKU5_ALKMQ | A6TKU5)
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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