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(-) Description

Title :  STRUCTURE OF UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH UTP
 
Authors :  C. Marco-Marin, V. Rubio
Date :  26 Feb 07  (Deposition) - 16 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Amino Acid Kinase, Phosphotranspherase, Allosteric Regulation, Pyrimidine Metabolism, Kinase, Ump Kinase, Transferase, Uridylate Kinase, Pyrimidine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Marco-Marin, V. Rubio
The Structure Of Ump Kinase From Pyrococcus Furiosus Complexed With Utp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1UTP6Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:43 , GLY B:44 , ARG B:49 , ILE B:52 , ASP B:66 , GLY B:69 , ILE B:70 , GLY B:113 , THR B:114 , HIS B:115 , PRO B:116 , HIS B:118 , THR B:119 , THR B:120 , VAL B:123 , HOH B:2001 , HOH B:2003 , HOH B:2004BINDING SITE FOR RESIDUE UTP B2000
2AC2SOFTWAREGLY A:43 , GLY A:44 , ARG A:49 , ASP A:66 , GLY A:69 , ILE A:70 , GLY A:113 , THR A:114 , HIS A:115 , HIS A:118 , THR A:119 , THR A:120 , VAL A:123 , HOH A:2001 , HOH A:2005 , HOH A:2006BINDING SITE FOR RESIDUE UTP A2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JI5)

(-) Exons   (0, 0)

(no "Exon" information available for 2JI5)

(-) 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:219
 aligned with PYRH_PYRFU | Q8U122 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:227
                              1                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       
           PYRH_PYRFU     - --MRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAMLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVMGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKMKPEELLEIVGKGIEKAGSSSVIDPLAAKIIARSGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
               SCOP domains d2ji5a_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....ee.......hhhhhhhhhhhhhh..eeeee.....................eehhhhhhhhhhh--------...hhhhhhhhhhhh..eeeehhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji5 A 998 SHMRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAMLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVMGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKMKPEELLEIVGK--------SVIDPLAAKIIARTGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168    |    -   |   188       198       208       218       
                             ||                                                                                                                                                                         173      182                                           
                           999|                                                                                                                                                                                                                                
                              1                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with PYRH_PYRFU | Q8U122 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:226
                             1                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
           PYRH_PYRFU     - -MRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAMLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVMGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKMKPEELLEIVGKGIEKAGSSSVIDPLAAKIIARSGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
               SCOP domains d2ji5b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -AA_kinase-2ji5B01 B:1-203                                                                                                                                                                                  ---------------------- Pfam domains (1)
           Pfam domains (2) -AA_kinase-2ji5B02 B:1-203                                                                                                                                                                                  ---------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....ee.......hhhhhhhhhhhhhh..eeeeee.........-----......eehhhhhhhhh.---------...hhhhhhhhhhhh..eeeee.hhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji5 B 999 HMRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAMLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVMGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTAD-----TAKKIKKMKPEELLEIVG---------SVIDPLAAKIIARTGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     | 159       169  |      -  |    189       199       209       219      
                          999|                                                                                                                                                 149   155              172       182                                           
                             1
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JI5)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: AA_kinase] (20)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRH_PYRFU | Q8U122)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0033862    UMP kinase activity    Catalysis of the reaction: ATP + UMP = ADP + UDP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    GO:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRH_PYRFU | Q8U122: 2bmu 2bri 2brx

(-) Related Entries Specified in the PDB File

2bmu UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP
2bri UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE ANALOG AMPPNP
2brx UMP KINASE FROM PYROCOCCUS FURIOSUS WITHOUT LIGANDS