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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOKINASE (TM0960) FROM THERMOTOGA MARITIMA AT 2.15 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  08 Sep 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm0960, Ribokinase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ribokinase (Tm0960) From Thermotoga Maritima At 2. 15 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOKINASE
    Chains: A, B
    EC Number: 2.7.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0960
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VM7)

(-) Sites  (0, 0)

(no "Site" information available for 1VM7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VM7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:159 -Pro A:160
2Ala B:159 -Pro B:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VM7)

(-) Exons   (0, 0)

(no "Exon" information available for 1VM7)

(-) 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:299
 aligned with Q9X055_THEMA | Q9X055 from UniProtKB/TrEMBL  Length:299

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
         Q9X055_THEMA     1 MFLVISVVGSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKIGEKGCRFVTCIGNDDYSDLLIENYEKLGITGYIRVSLPTGRAFIEVDKTGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIPFETTLECAKRFNGIVIFDPAPAQGINEEIFQYLDYLTPNEKEIEALSKDFFGEFLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFLKNL 299
               SCOP domains d1vm7a_ A: Ribokinase                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1vm7A00 A:1-299  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeeeee.........eee..eeeeeeehhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh.eeeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeee........hhhhhhhh.ee..hhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vm7 A   1 MFLVISVVGSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKIGEKGCRFVTCIGNDDYSDLLIENYEKLGITGYIRVSLPTGRAFIEVDKTGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIPFETTLECAKRFNGIVIFDPAPAQGINEEIFQYLDYLTPNEKEIEALSKDFFGEFLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFLKNL 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q9X055_THEMA | Q9X055 from UniProtKB/TrEMBL  Length:299

    Alignment length:297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
         Q9X055_THEMA     2 FLVISVVGSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKIGEKGCRFVTCIGNDDYSDLLIENYEKLGITGYIRVSLPTGRAFIEVDKTGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIPFETTLECAKRFNGIVIFDPAPAQGINEEIFQYLDYLTPNEKEIEALSKDFFGEFLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFLKN 298
               SCOP domains d1vm7b_ B: Ribokinase                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vm7B00 B:2-298  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -PfkB-1vm7B01 B:3-289                                                                                                                                                                                                                                                                           --------- Pfam domains (1)
           Pfam domains (2) -PfkB-1vm7B02 B:3-289                                                                                                                                                                                                                                                                           --------- Pfam domains (2)
         Sec.struct. author ...eeee...eeeeeee.........eee..eeeeeeehhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhheeeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeee........hhhhhhhh.ee..hhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vm7 B   2 FLVISVVGSSNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKIGEKGCRFVTCIGNDDYSDLLIENYEKLGITGYIRVSLPTGRAFIEVDKTGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIPFETTLECAKRFNGIVIFDPAPAQGINEEIFQYLDYLTPNEKEIEALSKDFFGEFLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSIPAREEVEAFLKN 298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X055_THEMA | Q9X055)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0004747    ribokinase activity    Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006014    D-ribose metabolic process    The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  Cis Peptide Bonds
    Ala A:159 - Pro A:160   [ RasMol ]  
    Ala B:159 - Pro B:160   [ RasMol ]  
 

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 Related Entries

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