1Q0N - JenaLib

Title :   CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF 6-HYDROXYMETHYL-7, 8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM E. COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.25 ANGSTROM RESOLUTION

Authors :   J. Blaszczyk, X. Ji

Date :   16 Jul 03 (Deposition) - 26 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

Chains :   Asym./Biol. Unit : A

Keywords :   Pyrophosphokinase, Pyrophosphoryl Transfer, Folate, Hppk, Pterin, 6-Hydroxymethyl-7, 8-Dihydropterin, Ternary Complex, Substrate Specificity, Antimicrobial Agent, Drug Design, X- Ray Crystallography, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Blaszczyk, G. Shi, H. Yan, X. Ji
Catalytic Center Assembly Of Hppk As Revealed By The Crystal Structure Of A Ternary Complex At 1. 25 A Resolution
Structure V. 8 1049 2000
PubMed-ID: 11080626 | Reference-DOI: 10.1016/S0969-2126(00)00502-5
(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 BL21(DE3)
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FOLK OR B0142
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- PYROPHOSPHOKINASE, HPPK, 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:95 , ASP A:97 , MG A:162 , APC A:171 , HOH A:212 , HOH A:226	BINDING SITE FOR RESIDUE MG A 161
2	AC2	SOFTWARE	ASP A:95 , ASP A:97 , MG A:161 , APC A:171 , PH2 A:181 , HOH A:216	BINDING SITE FOR RESIDUE MG A 162
3	AC3	SOFTWARE	PHE A:137 , PRO A:138 , ASP A:139 , HOH A:219 , HOH A:362	BINDING SITE FOR RESIDUE CL A 163
4	AC4	SOFTWARE	TYR A:116 , APC A:171 , HOH A:204 , HOH A:254 , HOH A:378	BINDING SITE FOR RESIDUE ACT A 164
5	AC5	SOFTWARE	GLU A:30 , SER A:31 , HIS A:32 , HOH A:341 , HOH A:438 , HOH A:470 , HOH A:475	BINDING SITE FOR RESIDUE ACT A 165
6	AC6	SOFTWARE	LEU A:11 , PRO A:51 , ALA A:65 , PRO A:66 , HOH A:266 , HOH A:318 , HOH A:331 , HOH A:350 , HOH A:428	BINDING SITE FOR RESIDUE ACT A 166
7	AC7	SOFTWARE	GLY A:46 , TRP A:89 , HOH A:415	BINDING SITE FOR RESIDUE ACT A 167
8	AC8	SOFTWARE	GLN A:74 , ARG A:84 , TRP A:89 , 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 , MG A:161 , MG A:162 , ACT A:164 , PH2 A:181 , HOH A:212 , HOH A:216 , HOH A:226 , HOH A:251 , HOH A:254 , HOH A:255 , HOH A:274 , HOH A:309 , HOH A:342 , HOH A:351 , HOH A:363 , HOH A:382	BINDING SITE FOR RESIDUE APC A 171
9	AC9	SOFTWARE	THR A:42 , PRO A:43 , LEU A:45 , TYR A:53 , ASN A:55 , TRP A:89 , ASP A:95 , PHE A:123 , MG A:162 , APC A:171 , HOH A:205 , HOH A:216 , HOH A:245 , HOH A:382	BINDING SITE FOR RESIDUE PH2 A 181

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)
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	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 d1q0na_ A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains 1q0nA00 A:1-158  [code=3.30.70.560, no name defined]                                                                                                           CATH domains
               Pfam domains ---HPPK-1q0nA01 A:4-131                                                                                                            --------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhh...eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhh..............eeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0n A   1 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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	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 (1, 1)

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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	1q0n
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1cbk	1CBK IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM H.INFLUENZAE WITH A 6-HYDROXYMETHYL-7,8- DIHYDROPTERINANALOG.
1dy3	1DY3 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPKFROM E.COLI WITH MGATP AND A 6-HYDROXYMETHYL-7,8- DIHYDROPTERIN ANALOG.
1eq0	1EQ0 IS THE SOLUTION STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPPCP.
1eqm	1EQM IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI WITH MGADP.
1eqo	1EQO IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8- DIHYDROPTERIN (OBSOLETE)
1ex8	1EX8 IS THE CRYSTAL STRUCTURE OF HPPK FROM E.COLI COMPLEXED WITH HP4A, A TWO-SUBSTRATE-MIMICKING INHIBITOR.
1f9h	1F9H IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(R92A) FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7, 8-DIHYDROPTERIN.
1f9y	1F9Y IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN.
1g4c	1G4C IS THE CRYSTAL STRUCTURE OF APO-HPPK(R92A) FROM E.COLI.
1hka	1HKA IS THE CRYSTAL STRUCTURE OF APO-HPPK FROM E.COLI.
1hq2	1HQ2 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(R82A) FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7, 8-DIHYDROPTERIN.
1im6	1IM6 IS THE CRYSTAL STRUCTURE OF APO-HPPK(R82A) FROM E.COLI.
1kbr	1KBR IS THE CRYSTAL STRUCTURE OF APO-HPPK(R92A) FROM E.COLI.

Description