Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF N TERMINAL REGION CONTAINING THE DIMERIZATION DOMAIN AND DNA BINDING DOMAIN OF HU PROTEIN(HISTONE LIKE PROTEIN-DNA BINDING) FROM MYCOBACTERIUM TUBERCULOSIS [H37RV]
 
Authors :  T. Bhowmick, U. A. Ramagopal, S. Ghosh, V. Nagaraja, S. Ramakumar
Date :  05 Feb 12  (Deposition) - 06 Feb 13  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Nucleoid Associated Protein, Nucleoid Architecture, Histone-Like, Hu, Hu-Ihf Fold, Genome Compaction, Gene Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Bhowmick, S. Ghosh, K. Dixit, V. Ganesan, U. A. Ramagopal, D. Dey, S. P. Sarma, S. Ramakumar, V. Nagaraja
Targeting Mycobacterium Tuberculosis Nucleoid-Associated Protein Hu With Structure-Based Inhibitors
Nat Commun V. 5 4124 2014
PubMed-ID: 24916461  |  Reference-DOI: 10.1038/NCOMMS5124

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN HU HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL BACTERIAL HISTONE-LIKE DOMAIN, UNP RESIDUES 1- 100
    Gene: HLP, HUP, HUPB, LBP21, MT3064, MTCY349.01, RV2986C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: 21 KDA LAMININ-2-BINDING PROTEIN, 28 KDA IRON-REGULATED PROTEIN, IREP-28, HISTONE-LIKE PROTEIN, HLP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:94 , HOH A:322BINDING SITE FOR RESIDUE MN A 201
2AC2SOFTWAREARG B:94 , GLU B:98 , HIS B:104BINDING SITE FOR RESIDUE MN B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DKY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DKY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DKY)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.DBH_MYCTO46-65
 		  2A:46-65
B:46-65
DBH_MYCTU46-65
 		  2A:46-65
B:46-65
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.DBH_MYCTO46-65
 		  2A:46-65
-
DBH_MYCTU46-65
 		  2A:46-65
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.DBH_MYCTO46-65
 		  2-
B:46-65
DBH_MYCTU46-65
 		  2-
B:46-65

(-) Exons   (0, 0)

(no "Exon" information available for 4DKY)

(-) 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:97
 aligned with DBH_MYCTO | P9WMK6 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            DBH_MYCTO     1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPA  97
               SCOP domains d4dkya_ A: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------HISTONE_LIKE        -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4dky A   1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPA  97
                                    10        20        30        40        50        60        70        80        90       


Chain A from PDB  Type:PROTEIN  Length:97
 aligned with DBH_MYCTU | P9WMK7 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            DBH_MYCTU     1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPA  97
               SCOP domains d4dkya_ A: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------HISTONE_LIKE        -------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4dky A   1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPA  97
                                    10        20        30        40        50        60        70        80        90       


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with DBH_MYCTO | P9WMK6 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
            DBH_MYCTO     1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPAEGPAVKR 104
               SCOP domains d4dkyb_ B: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh........---... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------HISTONE_LIKE        --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4dky B   1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPAE---HHH 104
                                    10        20        30        40        50        60        70        80        90       | - |  
                                                                                                                            98 102  


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with DBH_MYCTU | P9WMK7 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
            DBH_MYCTU     1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPAEGPAVKR 104
               SCOP domains d4dkyb_ B: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh........---... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------HISTONE_LIKE        --------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4dky B   1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPAE---HHH 104
                                    10        20        30        40        50        60        70        80        90       | - |  
                                                                                                                            98 102
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DKY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DKY)

(-) Gene Ontology  (13, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DBH_MYCTU | P9WMK7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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).
    GO:0097100    supercoiled DNA binding    Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.
biological process
    GO:0042262    DNA protection    Any process in which DNA is protected from damage by, for example, oxidative stress.
    GO:0010106    cellular response to iron ion starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of iron ions.
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0090143    nucleoid organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleoid. The nucleoid is the region of a bacterial cell, virion, mitochondrion or chloroplast to which the DNA is confined.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (DBH_MYCTO | P9WMK6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dky)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4dky
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DBH_MYCTO | P9WMK6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DBH_MYCTU | P9WMK7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DBH_MYCTO | P9WMK6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DBH_MYCTU | P9WMK7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DBH_MYCTO | P9WMK6: 4pt4
        DBH_MYCTU | P9WMK7: 4pt4

(-) Related Entries Specified in the PDB File

3c4i CRYSTAL STRUCTURE ANALYSIS OF N TERMINAL REGION CONTAINING THE DIMERIZATION DOMAIN AND DNA BINDING DOMAIN OF HU PROTEIN(HISTONE LIKE PROTEIN-DNA BINDING) FROM MYCOBACTERIUM TUBERCULOSIS [H37RV]