3HD1 - JenaLib

Title :   CRYSTAL STRUCTURE OF E. COLI HPPK(N10A) IN COMPLEX WITH MGAMPCPP

Authors :   J. Blaszczyk, Y. Li, H. Yan, X. Ji

Date :   06 May 09 (Deposition) - 19 May 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha Beta, Atp-Binding, Folate Biosynthesis, Kinase, Nucleotide- Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Blaszczyk, Y. Li, X. Ji, H. Yan
Role Of Loop Coupling In Enzymatic Catalysis And Conformational Dynamics
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE
	Chains	:	A
	EC Number	:	2.7.6.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B0142, FOIK, FOLK, JW0138
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Synonym	:	7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK, 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:95 , ASP A:97 , MG A:162 , APC A:171 , HOH A:201 , HOH A:202	BINDING SITE FOR RESIDUE MG A 161
2	AC2	SOFTWARE	ASP A:95 , ASP A:97 , MG A:161 , APC A:171 , HOH A:203 , HOH A:204	BINDING SITE FOR RESIDUE MG A 162
3	AC3	SOFTWARE	LYS A:23 , GLN A:74 , ARG A:92 , ASP A:95 , ASP A:97 , ILE A:98 , ARG A:110 , LEU A:111 , THR A:112 , HIS A:115 , TYR A:116 , ARG A:121 , HIS A:148 , MG A:161 , MG A:162 , HOH A:201 , HOH A:202 , HOH A:203 , HOH A:210 , HOH A:211 , HOH A:230 , HOH A:263 , HOH A:301 , HOH A:304 , HOH A:341 , HOH A:358 , HOH A:433 , HOH A:444	BINDING SITE FOR RESIDUE APC A 171
4	AC4	SOFTWARE	ARG A:84 , TRP A:89 , LYS A:157 , HOH A:297	BINDING SITE FOR RESIDUE CL A 191
5	AC5	SOFTWARE	TYR A:53 , ASN A:55 , PHE A:123 , HOH A:436 , HOH A:451	BINDING SITE FOR RESIDUE ACT A 192

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:158
 aligned with HPPK_ECOLI | P26281 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           HPPK_ECOLI     2 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 159
               SCOP domains d3hd1a_ A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains 3hd1A00 A:1-158  [code=3.30.70.560, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh...eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhhh..ee..ee....eeeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd1 A   1 TVAYIAIGSALASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HPPK_ECOLI | P26281)

molecular function
	GO:0003848	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity	Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + ATP = (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP + 2 H(+).
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
biological process
	GO:0046656	folic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	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:0046654	tetrahydrofolate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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