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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH BENM E226K MUTANT
 
Authors :  A. Ruangprasert, C. Momany, E. L. Neidle, S. H. Craven
Date :  28 Sep 09  (Deposition) - 29 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Hth, Lysr-Type Transcriptional Regulator, Activator, Aromatic Hydrocarbons Catabolism, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ruangprasert, S. H. Craven, E. L. Neidle, C. Momany
Structure Of Full-Length Benm
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ACIAD1435, BENM, BENR
    Mutation: YES
    Organism Scientific: ACINETOBACTER SP.
    Organism Taxid: 62977
    Strain: ADP1
    Synonym: BEN AND CAT OPERON TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3K1P)

(-) Sites  (0, 0)

(no "Site" information available for 3K1P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K1P)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:50 -Gly A:51
2Arg A:53 -Pro A:54
3Tyr A:195 -Pro A:196
4Lys A:200 -Pro A:201
5Arg B:50 -Gly B:51
6Arg B:53 -Pro B:54
7Tyr B:195 -Pro B:196
8Lys B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K1P)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.BENM_ACIAD1-58
 		  2A:1-58
B:1-58
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.BENM_ACIAD1-58
 		  2A:1-58
B:1-58
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.BENM_ACIAD1-58
 		  4A:1-58
B:1-58

(-) Exons   (0, 0)

(no "Exon" information available for 3K1P)

(-) 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:303
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   
           BENM_ACIAD     1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.................hhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_LYSR  PDB: A:1-58 UniProt: 1-58                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1p A   1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVRKVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   
           BENM_ACIAD     1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --HTH_1-3k1pB01 B:3-62                                        -----------------------LysR_substrate-3k1pB03 B:86-293                                                                                                                                                                                 ---------- Pfam domains (1)
           Pfam domains (2) --HTH_1-3k1pB02 B:3-62                                        -----------------------LysR_substrate-3k1pB04 B:86-293                                                                                                                                                                                 ---------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh..................hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhhh...eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhhh..eeeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_LYSR  PDB: B:1-58 UniProt: 1-58                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1p B   1 MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVSMTKRIASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVRKVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPN 303
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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 3K1P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K1P)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BENM_ACIAD | O68014)
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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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
    Arg A:50 - Gly A:51   [ RasMol ]  
    Arg A:53 - Pro A:54   [ RasMol ]  
    Arg B:50 - Gly B:51   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BENM_ACIAD | O68014: 2f6g 2f6p 2f78 2f7a 2f8d 2f97 2h99 2h9b 3k1m 3k1n 3m1e 4ihs 4iht

(-) Related Entries Specified in the PDB File

2f6g BENM EFFECTOR BINDING DOMAIN
2f97 BENM EFFECTOR BINDING DOMAIN, HIGH PH
2h99 BENM R156H MUTANT EFFECTOR BINDING DOMAIN
3glb CATM R156H MUTANT EFFECTOR BINDING DOMA
3k1m CRYSTAL STRUCTURE OF FULL-LENGTH BENM R156H MUTANT
3k1n CRYSTAL STRUCTURE OF FULL-LENGTH BENM