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(-) Description

Title :  STRUCTURE OF THE DOUBLE MUTANT (L6M; F134M, SEMET FORM) OF YQGF FROM ESCHERICHIA COLI, A HYPOTHETICAL PROTEIN
 
Authors :  A. Galkin, E. Sarikaya, W. Krajewski, A. Howard, O. Herzberg, Structure 2 Function Project (S2F)
Date :  30 Jan 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Hypothetical Protein, Yqgf, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Galkin, E. Sarikaya, W. Krajewski, A. Howard, O. Herzberg
Structure Of Yqgf From Escherichia Coli, A Hypothetical Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YQGF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYQGFM
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PET100/D-TOPO
    Gene: YQGF
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:78 , ARG A:82 , ARG B:97BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NU0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NU0)

(-) Exons   (0, 0)

(no "Exon" information available for 1NU0)

(-) 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:131
 aligned with YQGF_ECOLI | P0A8I1 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           YQGF_ECOLI     1 MSGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHGRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYFEQGY 138
               SCOP domains d1nu0a_ A: Hypothetical protein YqgF (RuvX)                                                                                                SCOP domains
               CATH domains -1nu0A00 A:2-138 Ribonuclease H-like (UPF0081)                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....eeeeeeee....eeeeeeeeeee..eehhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee......-------......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nu0 A   1 mSGTLmAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNmDGTEQPLTARARKFANRIHGRFGVEVKLHDERLSTVEA-------GGYRALNKGKVDSASAVIILESYmEQGY 138
                            |    |  10        20        30        40        50        60    |   70        80        90       100  |      -| ||   120       130   |    
                            |    |                                                         65-MSE                               103     110 ||                 134-MSE
                            1-MSE|                                                                                                        112|                        
                                 6-MSE                                                                                                     114                        


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with YQGF_ECOLI | P0A8I1 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           YQGF_ECOLI     2 SGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHGRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYFEQGY 138
               SCOP domains d1nu0b_ B: Hypothetical protein YqgF (RuvX)                                                                                               SCOP domains
               CATH domains 1nu0B00 B:2-138 Ribonuclease H-like (UPF0081)                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeeee.....eeeeeeeeee..eehhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhh..eeeee........-----------------..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nu0 B   2 SGTLmAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNmDGTEQPLTARARKFANRIHGRFGVEVKLHDERLSTVEA-----------------VDSASAVIILESYmEQGY 138
                                |   11        21        31        41        51        61   |    71        81        91       101 |       -       121       131  |    
                                6-MSE                                                     65-MSE                               103               121          134-MSE
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NU0)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YQGF_ECOLI | P0A8I1)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0000967    rRNA 5'-end processing    Any process involved in forming the mature 5' end of an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0031564    transcription antitermination    Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
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

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

UniProtKB/Swiss-Prot
        YQGF_ECOLI | P0A8I1: 1nmn 1ovq

(-) Related Entries Specified in the PDB File

1nmn NATIVE PROTEIN
yqgf