1RU1 - JenaLib

Title :   CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI HPPK(V83G/DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 1.40 ANGSTROM RESOLUTION (MONOCLINIC FORM)

Authors :   J. Blaszczyk, X. Ji

Date :   10 Dec 03 (Deposition) - 24 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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, Deletion Mutant, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Blaszczyk, Y. Li, Y. Wu, G. Shi, X. Ji, H. Yan
Essential Roles Of A Dynamic Loop In The Catalysis Of 6-Hydroxymethyl-7, 8-Dihydropterin Pyrophosphokinase.
Biochemistry V. 43 1469 2004
PubMed-ID: 14769023 | Reference-DOI: 10.1021/BI036053L
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 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:413 , HOH A:423	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:403	BINDING SITE FOR RESIDUE MG A 162
3	AC3	SOFTWARE	LYS A:119 , PHE A:137 , PRO A:138 , ASP A:139	BINDING SITE FOR RESIDUE CL A 163
4	AC4	SOFTWARE	ASP B:295 , ASP B:297 , MG B:362 , APC B:371 , HOH B:426 , HOH B:668	BINDING SITE FOR RESIDUE MG B 361
5	AC5	SOFTWARE	ASP B:295 , ASP B:297 , MG B:361 , APC B:371 , PH2 B:381 , HOH B:401	BINDING SITE FOR RESIDUE MG B 362
6	AC6	SOFTWARE	GLN A:74 , ASP A:95 , ASP A:97 , ILE A:98 , ARG A:110 , LEU A:111 , THR A:112 , VAL A:113 , HIS A:115 , TYR A:116 , ARG A:121 , MG A:161 , MG A:162 , PH2 A:181 , HOH A:403 , HOH A:413 , HOH A:423 , HOH A:442 , HOH A:473 , HOH A:539 , HOH A:540 , HOH A:651 , HOH A:681 , HOH A:682 , HOH A:798 , HOH A:818	BINDING SITE FOR RESIDUE APC A 171
7	AC7	SOFTWARE	THR A:42 , PRO A:43 , TYR A:53 , ASN A:55 , ASP A:95 , PHE A:123 , MG A:162 , APC A:171 , HOH A:403 , HOH A:640 , HOH A:708 , HOH A:713 , HOH A:818	BINDING SITE FOR RESIDUE PH2 A 181
8	AC8	SOFTWARE	LEU B:270 , ASP B:295 , ASP B:297 , ILE B:298 , ARG B:310 , LEU B:311 , THR B:312 , HIS B:315 , TYR B:316 , ARG B:321 , HIS B:348 , MG B:361 , MG B:362 , PH2 B:381 , HOH B:401 , HOH B:415 , HOH B:420 , HOH B:425 , HOH B:426 , HOH B:427 , HOH B:514 , HOH B:515 , HOH B:524 , HOH B:530 , HOH B:668 , HOH B:688 , HOH B:772	BINDING SITE FOR RESIDUE APC B 371
9	AC9	SOFTWARE	THR B:242 , PRO B:243 , LEU B:245 , TYR B:253 , ASN B:255 , ASP B:295 , PHE B:323 , MG B:362 , APC B:371 , HOH B:401 , HOH B:446 , HOH B:461 , HOH B:588	BINDING SITE FOR RESIDUE PH2 B 381

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:143
 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 d1ru1a_ A: 6-hydroxymethyl-7,8-dihydropterin       pyrophosphokinase, HPPK                                                                                     SCOP domains
               CATH domains 1ru1A00 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.---------...eeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ru1 A   1 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPP------PDYLNAAVALETSLAPEELLNHTQRIELQQGR---------RTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 158
                                    10        20        30        40   |     -|       60        70        80 |       - |     100       110       120       130       140       150        
                                                                      44     51                             82        92

Chain B from PDB  Type:PROTEIN  Length:152
 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 d1ru1b_ B: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains 1ru1B00 B:201-358  [code=3.30.70.560, no name defined]                                                                                                         CATH domains
           Pfam domains (1) ---HPPK-1ru1B01 B:204-331                                                                                                          --------------------------- Pfam domains (1)
           Pfam domains (2) ---HPPK-1ru1B02 B:204-331                                                                                                          --------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhh..eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhhh..------.....eeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ru1 B 201 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRG------GPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 358
                                   210       220       230       240       250       260       270       280  |    290       300       310       320       330       340       350        
                                                                                                            283    290

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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, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

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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Analysis Tools

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-DIHYDROPTERIN ANALOG.
1dy3	1DY3 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM 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.
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 HP FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8- PKDIHYDROPTERIN ANALOGS.
1g4c	1G4C IS THE CRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2+.
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.
1hq9	1HQ9 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE.
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.
1q0n	1Q0N IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8- DIHYDROPTERIN.
1rao	1RAO IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM E.COLI WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE.
1rb0	1RB0 IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI WITH 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE.
1rtz	1RTZ IS THE CRYSTAL STRUCTURE OF APO-HPPK(V83G/DEL84-89) DELETION MUTANT FROM E.COLI.
1ru2	CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/ DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN AT 1.48 ANGSTROM RESOLUTION (ORTHORHOMBIC FORM)

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