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(-) Description

Title :  STRUCTURE OF L-RHAMNULOSE KINASE IN COMPLEX WITH ADP AND BETA-L-RHAMNULOSE.
 
Authors :  D. Grueninger, G. E. Schulz
Date :  13 Apr 07  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Rhamnose Degradation, In-Line Phosphoryl Transfer, Hexokinase-Hsp70- Actin Superfamily, L-Rhamnulose Kinase, Rhamnose Metabolism, Kinase, Induced Fit, Transferase, Rare Sugars (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Grueninger, G. E. Schulz
Substrate Spectrum Of L-Rhamnulose Kinase Related To Models Derived From Two Ternary Complex Structures.
Febs Lett. V. 581 3127 2007
PubMed-ID: 17568582  |  Reference-DOI: 10.1016/J.FEBSLET.2007.05.075
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHAMNULOKINASE
    Chains: A
    EC Number: 2.7.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: JM105
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: BL21 (DE3)
    Synonym: L-RHAMNULOSE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2LRH1Ligand/Ion6-DEOXY-BETA-L-FRUCTOFURANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:82 , GLY A:83 , HIS A:236 , ASP A:237 , THR A:238 , TRP A:260 , ASN A:296 , HOH A:2069 , HOH A:2308 , HOH A:2309 , HOH A:2310BINDING SITE FOR RESIDUE LRH A1481
2AC2SOFTWAREGLY A:12 , ALA A:13 , SER A:14 , ARG A:17 , SER A:257 , GLY A:258 , THR A:259 , LEU A:300 , GLN A:304 , LEU A:315 , ILE A:319 , GLY A:402 , GLY A:403 , GLN A:405 , ASN A:406 , HOH A:2252 , HOH A:2308 , HOH A:2311 , HOH A:2312 , HOH A:2313 , HOH A:2314 , HOH A:2315 , HOH A:2316 , HOH A:2317 , HOH A:2318 , HOH A:2320BINDING SITE FOR RESIDUE ADP A1482

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:68 -A:222

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:424 -Pro A:425

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYT)

(-) 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:479
 aligned with RHAB_ECO57 | Q8X899 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:479
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471         
           RHAB_ECO57     2 TFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAIRLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGKRDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNATTTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTASAVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGLWLLQRVLQERQINDLPALISATQALPACRFIINPNDDRFINPETMCSEIQAACRETAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVARIHS 480
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---FGGY_N-2uytA02 A:5-244                                                                                                                                                                                                                          --------FGGY_C-2uytA01 A:253-441                                                                                                                                                                     --------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeeehhhheeeeeeeeeee...eee..eee.hhhhhhhhhhhhhhhhhhh.....eeeeee....eeee.....ee.......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhh.hhhhh........eeeeee.....eeeee....hhhhhhhhhh......eeeeee...eeeeeee.....hhhhhhhh.eee.hhhhheeeeeee..hhhhhhhhhhh...hhhhhhhhhh............hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eee.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyt A   2 TFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAIRLGLNKVCAAGIAIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGKRDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNATTTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTASAVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGLWLLQRVLQERQINDLPALIAATQALPACRFIINPNDDRFINPDEMCSEIQAACREMAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVALIHS 480
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471         


Chain A from PDB  Type:PROTEIN  Length:479
 aligned with RHAB_ECOUT | Q1R415 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:479
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471         
           RHAB_ECOUT     2 TFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWNVDSLESAIRLGLNKVCEEGIRIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGKRDIYQRSGIQFLPFNTIYQLRALTEQQPELIPHIAHALLIPDYFSYRLTGKMNWEYTNATTTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTASAVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGLWLLQRVLQERQINDLPALIAATQALPACRFIINPNDDRFINPDEMCSEIQAACRETAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVAQIHS 480
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---FGGY_N-2uytA02 A:5-244                                                                                                                                                                                                                          --------FGGY_C-2uytA01 A:253-441                                                                                                                                                                     --------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeeehhhheeeeeeeeeee...eee..eee.hhhhhhhhhhhhhhhhhhh.....eeeeee....eeee.....ee.......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhh.hhhhh........eeeeee.....eeeee....hhhhhhhhhh......eeeeee...eeeeeee.....hhhhhhhh.eee.hhhhheeeeeee..hhhhhhhhhhh...hhhhhhhhhh............hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eee.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyt A   2 TFRNCVAVDLGASSGRVMLARYERECRSLTLREIHRFNNGLHSQNGYVTWDVDSLESAIRLGLNKVCAAGIAIDSIGIDTWGVDFVLLDQQGQRVGLPVAYRDSRTNGLMAQAQQQLGKRDIYQRSGIQFLPFNTLYQLRALTEQQPELIPHIAHALLMPDYFSYRLTGKMNWEYTNATTTQLVNINSDDWDESLLAWSGANKAWFGRPTHPGNVIGHWICPQGNEIPVVAVASHDTASAVIASPLNGSRAAYLSSGTWSLMGFESQTPFTNDTALAANITNEGGAEGRYRVLKNIMGLWLLQRVLQERQINDLPALIAATQALPACRFIINPNDDRFINPDEMCSEIQAACREMAQPIPESDAELARCIFDSLALLYADVLHELAQLRGEDFSQLHIVGGGCQNTLLNQLCADACGIRVIAGPVEASTLGNIGIQLMTLDELNNVDDFRQVVSTTANLTTFTPNPDSEIAHYVALIHS 480
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471
   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  (0, 0)

(no "SCOP Domain" information available for 2UYT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (11, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHAB_ECO57 | Q8X899)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008993    rhamnulokinase activity    Catalysis of the reaction: ATP + L-rhamnulose = ADP + L-rhamnulose 1-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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
    GO:0019301    rhamnose catabolic process    The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
    GO:0019299    rhamnose metabolic process    The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.

Chain A   (RHAB_ECOUT | Q1R415)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008993    rhamnulokinase activity    Catalysis of the reaction: ATP + L-rhamnulose = ADP + L-rhamnulose 1-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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
    GO:0019301    rhamnose catabolic process    The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
    GO:0019299    rhamnose metabolic process    The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.

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  RHAB_ECOUT | Q1R415
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 Related Entries

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

UniProtKB/Swiss-Prot
        RHAB_ECO57 | Q8X899: 2cgj 2cgk 2cgl

(-) Related Entries Specified in the PDB File

2cgj CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN COMPLEX WITH L- FRUCTOSE AND ADP.
2cgk CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN AN OPEN UNCOMPLEXED CONFORMATION.
2cgl CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN COMPLEX WITH L- FRUCTOSE, ADP AND A MODELED ATP GAMMA PHOSPHATE.