1G4C - JenaLib

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Title :   CRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2+ AT 1.65 ANGSTROM RESOLUTION

Authors :   J. Blaszczyk, X. Ji

Date :   26 Oct 00 (Deposition) - 15 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

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

Reference :   J. Blaszczyk, Y. Li, G. Shi, H. Yan, X. Ji
Dynamic Roles Of Arginine Residues 82 And 92 Of Escherichia Coli 6-Hydroxymethyl-7, 8-Dihydropterin Pyrophosphokinase: Crystallographic Studies
Biochemistry V. 42 1573 2003
PubMed-ID: 12578370 | Reference-DOI: 10.1021/BI0267994
(for further references see the PDB file header)

Molecule 1 - 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
	Chains	:	A, B
	EC Number	:	2.7.6.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE, HPPK

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:486 , HOH A:504 , HOH A:540 , HOH B:451 , HOH B:517 , HOH B:544	BINDING SITE FOR RESIDUE MG A 361
2	AC2	SOFTWARE	GLU A:16 , HOH A:424 , HOH A:534 , ASP B:295 , ASP B:297 , MG B:363 , HOH B:406	BINDING SITE FOR RESIDUE MG B 362
3	AC3	SOFTWARE	HOH A:424 , ASP B:295 , ASP B:297 , MG B:362 , HOH B:431 , HOH B:466 , HOH B:545	BINDING SITE FOR RESIDUE MG B 363
4	AC4	SOFTWARE	LYS A:119 , PRO A:138 , ASP A:139 , HOH A:622	BINDING SITE FOR RESIDUE CL A 364
5	AC5	SOFTWARE	HOH A:794 , LYS B:319 , PRO B:338 , ASP B:339	BINDING SITE FOR RESIDUE CL B 365
6	AC6	SOFTWARE	TRP A:158 , HOH B:409 , HOH B:547	BINDING SITE FOR RESIDUE CL A 366

(no "SS Bond" information available for 1G4C)

Asymmetric Unit

No.	Residues
1	Val A:113	-	Pro A:114
2	Val B:313	-	Pro B:314

(no "SAP(SNP)/Variant" information available for 1G4C)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HPPK	PS00794	7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.	HPPK_ECOLI	89-100	2	A:88-99 B:288-299

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HPPK	PS00794	7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.	HPPK_ECOLI	89-100	1	A:88-99 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HPPK	PS00794	7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.	HPPK_ECOLI	89-100	1	- B:288-299

(no "Exon" information available for 1G4C)

Asymmetric Unit

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	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
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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 d1g4ca_ A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains 1g4cA00 A:1-158  [code=3.30.70.560, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhh..eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhhh..hhhhhh.....eeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g4c A   1 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPATLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B 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 d1g4cb_ B: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains 1g4cB00 B:201-358  [code=3.30.70.560, no name defined]                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh...eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g4c B 201 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPATLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 358
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.560, no name defined] (27)

Escherichia coli. Organism_taxid: 562. (10)

1a	1g4cA00	A:1-158
1b	1g4cB00	B:201-358

(no "Pfam Domain" information available for 1G4C)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	Cis Peptide Bonds
		Val A:113 - Pro A:114	[ RasMol ]
		Val B:313 - Pro B:314	[ RasMol ]

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	1g4c
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	HPPK_ECOLI \| P26281
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	2.7.6.3
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1cbk	THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM H.INFLUENZAE WITH A 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN ANALOG.
1dy3	THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH MGATP AND A 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN ANALOG.
1eq0	THE SOLUTION STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPPCP.
1eqm	THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI WITH MGADP.
1eqo	THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN.
1ex8	THE CRYSTAL STRUCTURE OF HPPK FROM E.COLI COMPLEXED WITH HP4A, A TWO-SUBSTRATE-MIMICKING INHIBITOR.
1f9h	THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(R92A) FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN
1hka	THE CRYSTAL STRUCTURE OF APO-HPPK FROM E.COLI.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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