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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCOPROTEIN ENDOPEPTIDASE (TM0874) FROM THERMOTOGA MARITIMA AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Jul 05  (Deposition) - 19 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Tm0874, Glycoprotein Endopeptidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, D. Mcmullan, L. Jaroszewski, S. S. Krishna, M. A. Elsliger, A. P. Yeh, P. Abdubek, T. Astakhova, H. L. Axelrod, D. Carlton, H. J. Chiu, T. Clayton, L. Duan, J. Feuerhelm, J. Grant, G. W. Han, K. K. Jin, H. E. Klock, M. W. Knuth, M. D. Miller, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, R. Reyes, C. L. Rife, H. Van Den Bedem, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structure Of An Essential Bacterial Protein Yeaz (Tm0874) From Thermotoga Maritima At 2. 5  A Resolution.
Acta Crystallogr. , Sect. F V. 66 1230 2010
PubMed-ID: 20944216  |  Reference-DOI: 10.1107/S1744309109022192

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TM0874
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0874
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: GLYCOPROTEIN ENDOPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2UNL4Ligand/IonUNKNOWN LIGAND
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (0, 0)

(no "Site" information available for 2A6A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A6A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:63 -Pro A:64
2Lys A:127 -Gly A:128
3Gly B:63 -Pro B:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A6A)

(-) Exons   (0, 0)

(no "Exon" information available for 2A6A)

(-) 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:193
 aligned with TSAB_THEMA | Q9WZX7 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
           TSAB_THEMA     1 MNVLALDTSQRIRIGLRKGEDLFEISYTGEKKHAEILPVVVKKLLDELDLKVKDLDVVGVGIGPGGLTGLRVGIATVVGLVSPYDIPVAPLNSFEMTAKSCPADGVVLVARRARKGYHYCAVYLKDKGLNPLKEPSVVSDEELEEITKEFSPKIVLKDDLLISPAVLVEESERLFREKKTIHYYEIEPLYLQK 193
               SCOP domains d2a6aa1 A:1-103 Hypothetical protein TM0874                                                            d2a6aa2 A:104-193 Hypothetical protein TM0874                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh.eeeee....hhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhh....eeeeeeee....eeeeeeeee....eeeeeeeeeehhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6a A   1 mNVLALDTSQRIRIGLRKGEDLFEISYTGEKKHAEILPVVVKKLLDELDLKVKDLDVVGVGIGPGGLTGLRVGIATVVGLVSPYDIPVAPLNSFEmTAKSCPADGVVLVARRARKGYHYCAVYLKDKGLNPLKEPSVVSDEELEEITKEFSPKIVLKDDLLISPAVLVEESERLFREKKTIHYYEIEPLYLQK 193
                            |       10        20        30        40        50        60        70        80        90     | 100       110       120       130       140       150       160       170       180       190   
                            |                                                                                             96-MSE                                                                                             
                            1-MSE                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with TSAB_THEMA | Q9WZX7 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:188
                             1                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
           TSAB_THEMA     - -MNVLALDTSQRIRIGLRKGEDLFEISYTGEKKHAEILPVVVKKLLDELDLKVKDLDVVGVGIGPGGLTGLRVGIATVVGLVSPYDIPVAPLNSFEMTAKSCPADGVVLVARRARKGYHYCAVYLKDKGLNPLKEPSVVSDEELEEITKEFSPKIVLKDDLLISPAVLVEESERLFREKKTIHYYEIE 187
               SCOP domains d2a6ab1 B:0-103 Hypothetical protein TM0874                                                             d2a6ab2 B:104-187 Hypothetical protein TM0874                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeehhhhhhhhh....eeeeeeeeee..eeeeeeeee...eeeeeeeeeeehhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6a B   0 HmNVLALDTSQRIRIGLRKGEDLFEISYTGEKKHAEILPVVVKKLLDELDLKVKDLDVVGVGIGPGGLTGLRVGIATVVGLVSPYDIPVAPLNSFEmTAKSCPADGVVLVARRARKGYHYCAVYLKDKGLNPLKEPSVVSDEELEEITKEFSPKIVLKDDLLISPAVLVEESERLFREKKTIHYYEIE 187
                             |       9        19        29        39        49        59        69        79        89      | 99       109       119       129       139       149       159       169       179        
                             1-MSE                                                                                         96-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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A6A)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TSAB_THEMA | Q9WZX7)
biological process
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002949    tRNA threonylcarbamoyladenosine modification    The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
cellular component
    GO:0000408    EKC/KEOPS complex    A protein complex involved in t6A tRNA modification; originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p.
    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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