2BRI - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE ANALOG AMPPNP

Authors :   C. Marco-Marin, F. Gil-Ortiz, V. Rubio

Date :   05 May 05 (Deposition) - 25 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 30)

No.	Name	Count	Type	Full Name
1	ANP	6	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:121 , SER A:182 , VAL A:183 , ANP A:1226	BINDING SITE FOR RESIDUE MG A1227
2	AC2	SOFTWARE	ASP B:121 , SER B:181 , SER B:182 , ASP B:185 , ANP B:1226	BINDING SITE FOR RESIDUE MG B1227
3	AC3	SOFTWARE	GLY A:8 , GLY A:9 , SER A:10 , GLY A:43 , GLY A:45 , 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 , MG A:1227	BINDING SITE FOR RESIDUE ANP A1226
4	AC4	SOFTWARE	GLY B:8 , GLY B:9 , SER B:10 , GLY B:43 , GLY B:44 , GLY B:45 , THR B:140 , ASN B:141 , GLY B:144 , TYR B:146 , ALA B:148 , ASP B:149 , ILE B:170 , SER B:181 , SER B:182 , VAL B:183 , MG B:1227 , HOH B:2005 , HOH B:2006	BINDING SITE FOR RESIDUE ANP B1226

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

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

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

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

(no "Exon" information available for 2BRI)

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 d2bria_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) -------hhhhhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......ee..hhhhhhhhhh...eee.......hhhhhhhhhhhhh...eeeeee....eee.........eeeeeehhhhhhhhh.............hhhhhhhhhhh..eeeeehhhhhhhhhhhhh.....eee.. Sec.struct. author (1)
     Sec.struct. author (2) eeeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bri 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: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 d2brib_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeee..........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
                 2bri B   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     
                            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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: PyrH-like (22)

Protein domain: automated matches (11)

Pyrococcus furiosus [TaxId: 2261] (4)

1a	d2bria_	A:
1b	d2brib_	B:

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

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

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ANP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bri)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2bri
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PYRH_PYRFU \| Q8U122
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.4.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PYRH_PYRFU \| Q8U122
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

2bmu	UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File