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(-) Description

Title :  CONSERVED HYPOTHETICAL PROTEIN CTH-95 FROM CLOSTRIDIUM THERMOCELLUM
 
Authors :  M. Zhao, W. Zhou, J. Chang, J. Habel, I. Kataeva, H. Xu, L. Chen, D. Lee, J. Nguyen, S. -H. Chang, P. Horanyi, Q. Florence, W. Tempel, D. Lin, H. Zhang, L. Ljundahl, Z. -J. Liu, J. Rose, B. -C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  21 Dec 04  (Deposition) - 01 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Conserved Hypothetical Protein, Clostridium Thermocellum, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zhao, W. Zhou, J. Chang, J. Habel, I. Kataeva, H. Xu, L. Chen, D. Lee, J. Nguyen, S. -H. Chang, P. Horanyi, Q. Florence, W. Tempel, D. Lin, H. Zhang, L. Ljundahl, Z. -J. Liu, J. Rose, B. -C. Wang
Conserved Hypothetical Protein Cth-95 From Clostridium Thermocellum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION ELONGATION FACTOR P
    Atcc27405
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificCLOSTRIDIUM THERMOCELLUM
    Organism Taxid1515
    SynonymEF-P, TRANSLATION INITIATION FACTOR 5A, EIF-5A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:89 , GLN A:90 , UNX A:1004 , PHE B:165 , ASN B:167BINDING SITE FOR RESIDUE UNX B 1001
2AC2SOFTWARELYS B:106 , GLU B:107BINDING SITE FOR RESIDUE UNX B 1002
3AC3SOFTWAREGLY B:17BINDING SITE FOR RESIDUE UNX B 1003
4AC4SOFTWAREGLU A:89 , GLN A:90 , UNX B:1001BINDING SITE FOR RESIDUE UNX A 1004
5AC5SOFTWAREARG A:173BINDING SITE FOR RESIDUE UNX A 1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EFPPS01275 Elongation factor P signature.EFP_CLOTH150-169
 
  2A:150-169
B:150-169

(-) Exons   (0, 0)

(no "Exon" information available for 1YBY)

(-) 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:176
 aligned with EFP_CLOTH | A3DDQ3 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
            EFP_CLOTH     1 MISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTDKMPKAHIERKDMQYLYNDGDLYYFMDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIEPPNFVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYMERV 185
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -1ybyA01 A:2-63  [code=2.30.30  .30, no name defined]          ----------------------------------------------------------------1ybyA03 A       :128-185 Nucleic acid-binding proteins     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhh....eeee..eeeeeeeeeee..--...eeeeeeee.....eeeeee....ee.....eeeeeeeeeee..eeeee......eeeeehhhhh..........eeeeeee..eeeeee...eeeeeeee.-------.....eeeeee....eeeee.......eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------EFP  PDB: A:150-169 ---------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yby A   1 mISAGDFKNGVTFELDGQIFQVIEFQHVKP--GAAFVRTKLKNIVTGATIEKTFNPTDKmPKAHIERKDmQYLYNDGDLYYFmDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIEPPNFVELEVTDT-------TATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYmERV 185
                            |       10        20        30  |     40        50        60        70        80  |     90       100       110       120       130     |   -   |   150       160       170       180 |   
                            |                           30 33                         60-MSE    70-MSE       83-MSE                                              136     144                                   182-MSE
                            1-MSE                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with EFP_CLOTH | A3DDQ3 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
            EFP_CLOTH     1 MISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTDKMPKAHIERKDMQYLYNDGDLYYFMDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIEPPNFVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYMERV 185
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -1ybyB01 B:2-63  [code=2.30.30.30, no name defined]            ----------------------------------------------------------------1ybyB03 B:128       -185 Nucleic acid-binding proteins     CATH domains
           Pfam domains (1) --EFP_N-1ybyB01 B:3-60                                      ------EFP-1ybyB03 B:67-121                                   -------Elong-fact-P       _C-1ybyB05 B:129-184                 - Pfam domains (1)
           Pfam domains (2) --EFP_N-1ybyB02 B:3-60                                      ------EFP-1ybyB04 B:67-121                                   -------Elong-fact-P       _C-1ybyB06 B:129-184                 - Pfam domains (2)
         Sec.struct. author .ee.hhh....eee....eeeeeeeeee.......eeeeeeee.....eeeeee....ee.....eeeeeeeeeee..eeeee......eeeeehhhhh..........eeeeee....eeeee...eeeeeeeee....-------.eeeeee....eeeee.......eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------EFP  PDB: B:150-169 ---------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yby B   1 mISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTDKmPKAHIERKDmQYLYNDGDLYYFmDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIEPPNFVELEVTDTEPGF-------ATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYmERV 185
                            |       10        20        30        40        50        60        70        80  |     90       100       110       120       130       140       150       160       170       180 |   
                            |                                                         60-MSE    70-MSE       83-MSE                                                  140     148                               182-MSE
                            1-MSE                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 1YBY)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: KOW (56)
(-)
Clan: OB (224)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (EFP_CLOTH | A3DDQ3)
molecular function
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0043043    peptide biosynthetic process    The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
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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