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(-) Description

Title :  UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP
 
Authors :  C. Marco-Marin, F. Gil-Ortiz, V. Rubio
Date :  16 Mar 05  (Deposition) - 25 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Ump Kinase, Amino Acid Kinase, Phosphoryl Group Transfer, Pyrimidine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Marco-Marin, F. Gil-Ortiz, V. Rubio
The Crystal Structure Of Pyrococcus Furiosus Ump Kinase Provides Insight Into Catalysis And Regulation In Microbial Pyrimidine Nucleotide Biosynthesis.
J. Mol. Biol. V. 352 438 2005
PubMed-ID: 16095620  |  Reference-DOI: 10.1016/J.JMB.2005.07.045

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUKPFU
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    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  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1ANP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
4U5P6Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:6 , THR A:120 , ASP A:121 , ANP A:1226 , HOH A:2001BINDING SITE FOR RESIDUE MG A1228
2AC2SOFTWAREASP A:121 , SER A:182 , ANP A:1226BINDING SITE FOR RESIDUE MG A1229
3AC3SOFTWAREASP B:6 , THR B:120 , ASP B:121 , ANP B:2000 , HOH B:2023BINDING SITE FOR RESIDUE MG B1229
4AC4SOFTWAREASP B:121 , SER B:182 , VAL B:183 , ANP B:2000BINDING SITE FOR RESIDUE MG B2002
5AC5SOFTWAREGLY A:8 , GLY A:9 , SER A:10 , GLY A:43 , GLY A:44 , GLY A:45 , ARG A:49 , THR A:120 , THR A:140 , ASN A:141 , VAL A:142 , GLY A:144 , TYR A:146 , ALA A:148 , ASP A:149 , PRO A:150 , LYS A:151 , SER A:181 , SER A:182 , VAL A:183 , U5P A:1227 , MG A:1228 , MG A:1229 , HOH A:2033BINDING SITE FOR RESIDUE ANP A1226
6AC6SOFTWAREGLY A:44 , GLY A:45 , ASP A:66 , GLY A:69 , ILE A:70 , GLY A:113 , THR A:114 , HIS A:115 , PRO A:116 , HIS A:118 , THR A:119 , THR A:120 , VAL A:123 , ALA A:178 , GLY A:179 , ANP A:1226 , HOH A:2033BINDING SITE FOR RESIDUE U5P A1227
7AC7SOFTWAREGLY B:8 , GLY B:9 , SER B:10 , GLY B:43 , GLY B:44 , GLY B:45 , THR B:120 , THR B:140 , ASN B:141 , VAL B:142 , GLY B:144 , VAL B:145 , TYR B:146 , ALA B:148 , ASP B:149 , PRO B:150 , SER B:181 , SER B:182 , VAL B:183 , MG B:1229 , U5P B:2001 , MG B:2002 , HOH B:2021BINDING SITE FOR RESIDUE ANP B2000
8AC8SOFTWAREGLY B:43 , GLY B:44 , GLY B:45 , 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 , ALA B:178 , GLY B:179 , SER B:180 , ANP B:2000BINDING SITE FOR RESIDUE U5P B2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BMU)

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

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           PYRH_PYRFU     1 MRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAMLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVMGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKMKPEELLEIVGKGIEKAGSSSVIDPLAAKIIARSGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
               SCOP domains d2bmua_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeehhhhhh....hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh......ee..hhhhhhhhhh...eee.......hhhhhhhhhhhhhh..eeeee.....ee..........eeeeeehhhhhhhhh.............hhhhhhhhhhh..eeeeehhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmu A   1 mRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAmLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVmGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKmKPEELLEIVGKGIEKAGSSSVIDPLAAKIIARSGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
                            |       10        20        30        40        50        60        70       |80        90       100       110|      120       130       140       150       160 |     170       180       190       200       210       220     
                            |                                                                           78-MSE                          111-MSE                                            162-MSE                                                           
                            1-MSE                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:226
 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 d2bmub_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..........hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh......ee..hhhhhhhhhh....ee.......hhhhhhhhhhhhhh..eeeee.....ee..........eeeeeehhhhhhhhh.............hhhhhhhhhhh..eeeeehhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmu B   0 AmRIVFDIGGSVLVPENPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYIEVAEKFNSSETFKDFIGIQITRANAmLLIAALREKAYPVVVEDFWEAWKAVQLKKIPVmGGTHPGHTTDAVAALLAEFLKADLLVVITNVDGVYTADPKKDPTAKKIKKmKPEELLEIVGKGIEKAGSSSVIDPLAAKIIARSGIKTIVIGKEDAKDLFRVIKGDHNGTTIEP 225
                             |       9        19        29        39        49        59        69        79        89        99       109 |     119       129       139       149       159  |    169       179       189       199       209       219      
                             1-MSE                                                                       78-MSE                          111-MSE                                            162-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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

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UniProtKB/Swiss-Prot
        PYRH_PYRFU | Q8U122: 2bri 2brx 2ji5

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