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(-) Description

Title :  X-RAY STRUCTURE OF TM1055 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET VT76
 
Authors :  A. P. Kuzin, Y. Chen, A. Edwards, T. Skarina, A. Savchenko, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  04 Nov 03  (Deposition) - 02 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, A. Edwards, T. Skarina, A. Savchenko, L. Tong
X-Ray Structure Of Tm1055 Northeast Structural Genomics Consortium Target Vt76
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN VT76
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)*
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1RCU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:16 -Pro A:17
2Ser B:16 -Pro B:17
3Ser C:16 -Pro C:17
4Ser D:16 -Pro D:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RCU)

(-) 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:170
 aligned with Q9X0E5_THEMA | Q9X0E5 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q9X0E5_THEMA     1 MKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVMELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQMRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
               SCOP domains d1rcua_ A: Hypothetical protein TM1055                                                                                                                                     SCOP domains
               CATH domains -1rcuA00 A:2-170  [code=3.40.50.450, no name defined]                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh...eeeee...........eeee...hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rcu A   1 mKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVmELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQmRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
                            |       10        20        30        40       |50        60        70        80       |90       100       110       120       130       140       150       160       170
                            |                                             48-MSE                                  88-MSE                                                                              
                            1-MSE                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q9X0E5_THEMA | Q9X0E5 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q9X0E5_THEMA     1 MKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVMELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQMRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
               SCOP domains d1rcub_ B: Hypothetical protein TM1055                                                                                                                                     SCOP domains
               CATH domains -1rcuB00 B:2-170  [code=3.40.50.450, no name defined]                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh...eeeee...........eeee...hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rcu B   1 mKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVmELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQmRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
                            |       10        20        30        40       |50        60        70        80       |90       100       110       120       130       140       150       160       170
                            1-MSE                                         48-MSE                                  88-MSE                                                                              


Chain C from PDB  Type:PROTEIN  Length:170
 aligned with Q9X0E5_THEMA | Q9X0E5 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q9X0E5_THEMA     1 MKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVMELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQMRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
               SCOP domains d1rcuc_ C: Hypothetical protein TM1055                                                                                                                                     SCOP domains
               CATH domains -1rcuC00 C:2-170  [code=3.40.50.450, no name defined]                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh...eeeee...........eeee...hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhhh.............eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rcu C   1 mKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVmELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQmRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
                            |       10        20        30        40       |50        60        70        80       |90       100       110       120       130       140       150       160       170
                            1-MSE                                         48-MSE                                  88-MSE                                                                              


Chain D from PDB  Type:PROTEIN  Length:170
 aligned with Q9X0E5_THEMA | Q9X0E5 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q9X0E5_THEMA     1 MKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVMELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQMRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
               SCOP domains d1rcud_ D: Hypothetical protein TM1055                                                                                                                                     SCOP domains
               CATH domains -1rcuD00 D:2-170  [code=3.40.50.450, no name defined]                                                                                                                      CATH domains
           Pfam domains (1) -----------------------------------------------Lysine_decarbox-1rcuD01 D:48-167                                                                                        --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Lysine_decarbox-1rcuD02 D:48-167                                                                                        --- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------Lysine_decarbox-1rcuD03 D:48-167                                                                                        --- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------Lysine_decarbox-1rcuD04 D:48-167                                                                                        --- Pfam domains (4)
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh...eeeee...........eeee...hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rcu D   1 mKKVVVVGYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNGGRDGVmELVSQGVREAGGTVVGILPDEEAGNPYLSVAVKTGLDFQmRSFVLLRNADVVVSIGGEIGTAIEILGAYALGKPVILLRGTGGWTDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170
                            |       10        20        30        40       |50        60        70        80       |90       100       110       120       130       140       150       160       170
                            1-MSE                                         48-MSE                                  88-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: DprA (10)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9X0E5_THEMA | Q9X0E5)
molecular function
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
biological process
    GO:0009691    cytokinin biosynthetic process    The chemical reactions and pathways resulting in the formation of cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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vt76