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Title :   THE CRYSTAL STRUCTURE OF UMP KINASE FROM BACILLUS ANTHRACIS (BA1797)

Authors :   C. Meier, L. G. Carter, E. J. Mancini, R. J. Owens, D. I. Stuart, R. M. Esno Protein Production Facility (Oppf), Structural Proteomics In (Spine)

Date :   23 Apr 08 (Deposition) - 29 Jul 08 (Release) - 24 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.82

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)

Keywords :   Structural Genomics, Pyrimidine Biosynthesis, Atp-Binding, Uridylate Kinase, Nucleotide-Binding, Oppf, Pyrh, Kinase, Cytoplasm, Transferase, Oxford Protein Production Facility (Oppf), Structural Proteomics In Europe (Spine) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Meier, L. G. Carter, S. Sainsbury, E. J. Mancini, R. J. Owens, D. I. Stuart, R. M. Esnouf
The Crystal Structure Of Ump Kinase From Bacillus Anthracis (Ba1797) Reveals An Allosteric Nucleotide-Binding Site.
J. Mol. Biol. V. 381 1098 2008
PubMed-ID: 18625239 | Reference-DOI: 10.1016/J.JMB.2008.06.078

Molecule 1 - URIDYLATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	GATEWAY
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector	:	PDEST14
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	198094
	Strain	:	AMES
	Synonym	:	UMP KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ATP	3	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	ATP	6	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:99 , ASN A:107 , ALA A:108 , ALA A:110 , PRO A:112 , ARG A:117 , TYR A:126 , HOH A:2047 , HOH A:2048 , ILE B:114 , LEU B:116 , ARG B:117 , HIS B:120 , HOH B:2047 , MG C:1247	BINDING SITE FOR RESIDUE ATP A1246
2	AC2	SOFTWARE	ARG A:117 , HIS A:120 , HOH A:2048 , ATP B:1246 , ARG C:99 , ASN C:107 , ALA C:108 , ALA C:110 , GLU C:111 , PRO C:112 , ARG C:117 , TYR C:126 , MG C:1247	BINDING SITE FOR RESIDUE ATP C1246
3	AC3	SOFTWARE	ARG B:99 , ASN B:107 , ALA B:108 , ALA B:110 , GLU B:111 , ARG B:117 , TYR B:126 , HOH B:2047 , ILE C:114 , ARG C:117 , HIS C:120 , ATP C:1246 , MG C:1247	BINDING SITE FOR RESIDUE ATP B1246
4	AC4	SOFTWARE	ATP A:1246 , HOH A:2048 , ATP B:1246 , ATP C:1246	BINDING SITE FOR RESIDUE MG C1247

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

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

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

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

(no "Exon" information available for 2JJX)

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:244
 aligned with Q81S73_BACAN | Q81S73 from UniProtKB/TrEMBL  Length:247

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
         Q81S73_BACAN     2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
               SCOP domains d2jjxa_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 2jjxA00 A:2-245  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhh........hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee.........hhhhhhhhhhhh...eeeeee.....................eeehhhhhhh.....hhhhhhhhhhhh..eeeee....hhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjx A   2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with Q81S73_BACAN | Q81S73 from UniProtKB/TrEMBL  Length:247

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
         Q81S73_BACAN     2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
               SCOP domains d2jjxb_ B: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 2jjxB00 B:2-245  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee.........hhhhhhhhhhhh...eeeeee.....................eeehhhhhhh.....hhhhhhhhhhhh..eeeee....hhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjx B   2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain C from PDB  Type:PROTEIN  Length:244
 aligned with Q81S73_BACAN | Q81S73 from UniProtKB/TrEMBL  Length:247

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
         Q81S73_BACAN     2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
               SCOP domains d2jjxc_ C: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 2jjxC00 C:2-245  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---AA_kinase-2jjxC01 C:5-216                                                                                                                                                                                           ----------------------------- Pfam domains (1)
           Pfam domains (2) ---AA_kinase-2jjxC02 C:5-216                                                                                                                                                                                           ----------------------------- Pfam domains (2)
           Pfam domains (3) ---AA_kinase-2jjxC03 C:5-216                                                                                                                                                                                           ----------------------------- Pfam domains (3)
         Sec.struct. author ....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee.........hhhhhhhhhhhh...eeeeee.....................eeehhhhhhh.....hhhhhhhhhhhh..eeeee....hhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jjx C   2 RPYKRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGGGNIFRGHLAEEWGIDRVEADNIGTLGTIINSLMLRGVLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHLDNGYIVIFGGGNGQPFVTTDYPSVQRAIEMNSDAILVAKQGVDGVFTSDPKHNKSAKMYRKLNYNDVVRQNIQVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLLVH 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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: automated matches (24)

Protein domain: automated matches (24)

Bacillus anthracis [TaxId: 198094] (1)

1a	d2jjxa_	A:
1b	d2jjxb_	B:
1c	d2jjxc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Carbamate kinase (24)

Homologous Superfamily: [code=3.40.1160.10, no name defined] (24)

Bacillus anthracis. Organism_taxid: 198094. Strain: ames. (1)

1a	2jjxA00	A:2-245
1b	2jjxB00	B:2-245
1c	2jjxC00	C:2-245

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: AA_kinase (20)

Bacillus anthracis (1)

1a	AA_kinase-2jjxC01	C:5-216
1b	AA_kinase-2jjxC02	C:5-216
1c	AA_kinase-2jjxC03	C:5-216

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q81S73_BACAN | Q81S73)

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: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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		Biological Unit 1	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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