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(-) Description

Title :  C-TERMINAL DOMAIN HEXAMER OF AHRC BOUND WITH L-ARGININE
 
Authors :  J. A. Garnett, S. Baumberg, P. G. Stockley, S. E. V. Phillips
Date :  15 Mar 07  (Deposition) - 30 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Alpha-Beta, L-Arginine Binding Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Garnett, S. Baumberg, P. G. Stockley, S. E. Phillips
Structure Of The C-Terminal Effector-Binding Domain Of Ahrc Bound To Its Corepressor L-Arginine.
Acta Crystallogr. , Sect. F V. 63 918 2007
PubMed-ID: 18007040  |  Reference-DOI: 10.1107/S1744309107049391
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE REPRESSOR
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (RESIDUES 67-149)
    Gene: ARGR, AHRC
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: ARGININE HYDROXAMATE RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ARG5Mod. Amino AcidARGININE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1ARG10Mod. Amino AcidARGININE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:100 , GLY A:101 , GLY A:124 , ASP A:125 , ASP A:126 , THR A:127 , GLN B:104 , ALA B:108 , ASP B:111 , THR B:121 , CYS B:123 , HOH B:216 , HOH B:238BINDING SITE FOR RESIDUE ARG B 201
2AC2SOFTWAREGLY B:124 , ASP B:125 , ASP B:126 , THR B:127 , ARG B:203 , HOH B:234 , HOH B:249 , PRO C:100 , GLY C:101 , GLN C:104 , ALA C:108 , ASP C:111 , THR C:121 , CYS C:123 , ASP C:125BINDING SITE FOR RESIDUE ARG B 202
3AC3SOFTWAREGLN A:104 , ALA A:108 , ASP A:111 , THR A:121 , ILE A:122 , CYS A:123 , PRO B:100 , GLY B:101 , ASP B:125 , ARG B:202 , HOH B:209 , HOH B:227 , GLY C:124 , ASP C:125 , ASP C:126 , THR C:127BINDING SITE FOR RESIDUE ARG B 203
4AC4SOFTWAREGLU A:147 , LEU A:149 , ASP B:116 , HOH B:211BINDING SITE FOR RESIDUE ARG B 204
5AC5SOFTWAREGLU A:147 , ASP B:137BINDING SITE FOR RESIDUE ARG B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P5M)

(-) Exons   (0, 0)

(no "Exon" information available for 2P5M)

(-) 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:82
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:82
                                    77        87        97       107       117       127       137       147  
           ARGR_BACSU    68 QRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d2p5ma_ A: C-terminal domain of arginine repressor                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeeeeee..eeeeee...hhhhhhhhhhh.......eeee...eeeee..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2p5m A  68 QRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    77        87        97       107       117       127       137       147  


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:84
                                                                                                        149     
                                    80        90       100       110       120       130       140        |-    
           ARGR_BACSU    71 NPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL-----   -
               SCOP domains d2p5mb_ B: C-terminal domain of arginine repressor                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeee..eeeeee...hhhhhhhhhhh.......eeee...eeeee..hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2p5m B  71 NPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELLRRRRR 205
                                    80        90       100       110       120       130       140       201    
                                                                                                        149|    
                                                                                                         201    


Chain C from PDB  Type:PROTEIN  Length:79
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:79
                                    80        90       100       110       120       130       140         
           ARGR_BACSU    71 NPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d2p5mc_ C: C-terminal domain of arginine repressor                              SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Arg_repressor_C-2p5mC01 C:79-148                                      - Pfam domains (1)
           Pfam domains (2) --------Arg_repressor_C-2p5mC02 C:79-148                                      - Pfam domains (2)
           Pfam domains (3) --------Arg_repressor_C-2p5mC03 C:79-148                                      - Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhheeeeeee..eeeeee...hhhhhhhhhhhhh...eeeeee...eeeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 2p5m C  71 NPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    80        90       100       110       120       130       140
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P5M)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Arg_repressor_C] (6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ARGR_BACSU | P17893)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034618    arginine binding    Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic 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:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0019547    arginine catabolic process to ornithine    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        ARGR_BACSU | P17893: 1f9n 2p5k 2p5l

(-) Related Entries Specified in the PDB File

2p5k 2p5l