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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI HFQ, IN COMPLEX WITH ATP
 
Authors :  M. Beich-Frandsen, B. Vecerek, H. Hammele, K. Kloiber, B. Sjoeblom, U. K. Djinovic-Carugo
Date :  09 Feb 11  (Deposition) - 15 Feb 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rna Binding Protein, Sm-Like, Pleiotropic Regulator, Rna Chaperone, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hammerle, M. Beich-Frandsen, B. Vecerek, L. Rajkowitsch, O. Carugo, K. Djinovic-Carugo, U. Blasi
Structural And Biochemical Studies On Atp Binding And Hydrolysis By The Escherichia Coli Rna Chaperone Hfq
Plos One V. 7 50892 2012
PubMed-ID: 23226421  |  Reference-DOI: 10.1371/JOURNAL.PONE.0050892

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL (L)SM CORE-DOMAIN, UNP RESIDUES 1-65
    Gene: B4172, HFQ, JW4130
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: HF-1, HOST FACTOR-I PROTEIN, HF-I

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:25 , GLY A:29 , SER A:60 , THR A:61 , HOH A:69 , HOH A:202 , LEU B:26 , ILE B:30 , LYS B:31 , LEU B:32 , GLN B:52 , HOH B:69 , ARG E:19BINDING SITE FOR RESIDUE ATP A 66
2AC2SOFTWARETYR B:25 , GLY B:29 , LYS B:31 , THR B:61 , HOH B:229 , HOH B:231 , HOH B:237 , HOH B:242 , ILE C:30 , LEU C:32 , GLN C:52BINDING SITE FOR RESIDUE ATP B 66
3AC3SOFTWARETYR C:25 , GLY C:29 , LYS C:31 , THR C:61 , ILE D:30 , LEU D:32 , GLN D:52BINDING SITE FOR RESIDUE ATP C 66
4AC4SOFTWAREARG B:19 , TYR D:25 , GLY D:29 , LYS D:31 , SER D:60 , THR D:61 , HOH D:206 , LEU E:26 , ILE E:30 , LEU E:32 , HOH E:182BINDING SITE FOR RESIDUE ATP D 66

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QO3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:48 -Thr B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QO3)

(-) Exons   (0, 0)

(no "Exon" information available for 3QO3)

(-) 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:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3a_ A: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 A  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain B from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3b_ B: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeee.....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 B  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain C from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3c_ C: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 C  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain D from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3d_ D: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 D  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain E from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3e_ E: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 E  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain F from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3qo3f_ F: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qo3 F  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QO3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QO3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (HFQ_ECOLI | P0A6X3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003681    bent DNA binding    Interacting selectively and non-covalently with DNA in a bent conformation.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0040033    negative regulation of translation, ncRNA-mediated    Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein.
    GO:0045975    positive regulation of translation, ncRNA-mediated    Any process, mediated by small non-coding RNAs, that activates or increases the rate that mRNAs are effectively translated into protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_ECOLI | P0A6X3: 1hk9 1m7c 1oou 1oov 2y90 2yht 3gib 3qhs 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

3qhs