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(-) Description

Title :  CRYSTAL STRUCTURE OF PH1519 FROM PYROCOCCUS HORIKOSII OT3
 
Authors :  N. Okazaki, N. Nakano, A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Jul 05  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Structural Genomics, Pyrococcus Horikosii Ot3, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Okazaki, N. Nakano, A. Shinkai, S. Yokoyama
Crystal Structure Of Ph1519 From Pyrococcus Horikosii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR PH1519
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GLN1Mod. Amino AcidGLUTAMINE
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GLN2Mod. Amino AcidGLUTAMINE
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GLN1Mod. Amino AcidGLUTAMINE
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:146 , HOH A:2007 , HOH A:2046BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREGLY A:64 , SER A:66 , LYS A:112 , HOH A:2018 , HOH A:2098 , HOH A:2138BINDING SITE FOR RESIDUE CA A 2002
3AC3SOFTWARESER A:66 , HOH A:2029BINDING SITE FOR RESIDUE CA A 2003
4AC4SOFTWAREHOH A:2054 , HOH A:2140 , HOH A:2217 , HOH A:2218BINDING SITE FOR RESIDUE CA A 2004
5AC5SOFTWAREGLU A:61 , SER A:66 , LEU A:68 , ARG A:110 , SER A:114 , VAL A:138 , LEU A:139 , THR A:141 , HOH A:2020 , HOH A:2024 , HOH A:2213BINDING SITE FOR RESIDUE GLN A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ASNC_2PS50956 AsnC-type HTH domain profile.REG6_PYRHO5-66  1A:5-66
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ASNC_2PS50956 AsnC-type HTH domain profile.REG6_PYRHO5-66  2A:5-66
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ASNC_2PS50956 AsnC-type HTH domain profile.REG6_PYRHO5-66  1A:5-66

(-) Exons   (0, 0)

(no "Exon" information available for 2CYY)

(-) 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:152
 aligned with REG6_PYRHO | O59188 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:152
                                                                                                                                                                                151 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150| 
          REG6_PYRHO      1 MRVPLDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGYSMLAFILVKVKAGKYSEVASNLAKYPEIVEVYETTGDYDMVVKIRTKNSEELNNFLDLIGSIPGVEGTHTMIVLKTHKETTELPIK-    -
               SCOP domains d2cyya1 A:1-64 automated matches                                d2cyya2 A:65-151 automated matches                                                     - SCOP domains
               CATH domains -2cyyA01 A:2-56                                         2cyyA02 A:57-151  [code=3.30.70.920, no name defined]                                          - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhh..eeeeeeeee...hhhhhhhhhhh...eeeeee......eeeeeee.hhhhhhhhhhhhhh...eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_ASNC_2  PDB: A:5-66 UniProt: 5-66                         -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cyy A    1 mRVPLDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGYSmLAFILVKVKAGKYSEVASNLAKYPEIVEVYETTGDYDmVVKIRTKNSEELNNFLDLIGSIPGVEGTHTmIVLKTHKETTELPIKQ 1001
                            |       10        20        30        40        50        60      | 70        80        90       100    |  110       120       130     | 140       150||
                            |                                                                67-MSE                               105-MSE                        136-MSE        151|
                            1-MSE                                                                                                                                               1001
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CYY)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (REG6_PYRHO | O59188)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  2cyy
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  REG6_PYRHO | O59188
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 Related Entries

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

UniProtKB/Swiss-Prot
        REG6_PYRHO | O59188: 1ri7 2e1c 2zny 2znz

(-) Related Entries Specified in the PDB File

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