2O5W - JenaLib

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Title :   STRUCTURE OF THE E. COLI DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHOHYDROLASE IN COMPLEX WITH SM+3 AND PYROPHOSPHATE

Authors :   S. B. Gabelli, M. A. Bianchet, L. M. Amzel

Date :   06 Dec 06 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Dihydroneopterin Triphosphate Pyrophosphohydrolase Nudix Nucleoside Triphosphate Pyrophosphohydrolase Mutt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Gabelli, M. A. Bianchet, W. Xu, C. A. Dunn, Z. D. Niu, L. M. Amzel, M. J. Bessman
Structure And Function Of The E. Coli Dihydroneopterin Triphosphate Pyrophosphatase: A Nudix Enzyme Involved In Folate Biosynthesis.
Structure V. 15 1014 2007
PubMed-ID: 17698004 | Reference-DOI: 10.1016/J.STR.2007.06.018
(for further references see the PDB file header)

Molecule 1 - DATP PYROPHOSPHOHYDROLASE
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11B
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NUDB, NTPA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	PPV	2	Ligand/Ion	PYROPHOSPHATE
3	SM	3	Ligand/Ion	SAMARIUM (III) ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	PPV	1	Ligand/Ion	PYROPHOSPHATE
3	SM	-1	Ligand/Ion	SAMARIUM (III) ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	PPV	-1	Ligand/Ion	PYROPHOSPHATE
3	SM	-1	Ligand/Ion	SAMARIUM (III) ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	PPV	1	Ligand/Ion	PYROPHOSPHATE
3	SM	-1	Ligand/Ion	SAMARIUM (III) ION
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	PPV	-1	Ligand/Ion	PYROPHOSPHATE
3	SM	-1	Ligand/Ion	SAMARIUM (III) ION
4	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:4 , LYS A:7 , ARG A:90 , PPV A:163	BINDING SITE FOR RESIDUE SO4 A 164
02	AC2	SOFTWARE	GLU A:80 , PHE A:81 , GLU A:82 , ARG A:97 , TRP A:136 , HOH A:192	BINDING SITE FOR RESIDUE SO4 A 165
03	AC3	SOFTWARE	LYS B:4 , LYS B:7 , ARG B:90	BINDING SITE FOR RESIDUE SO4 B 164
04	AC4	SOFTWARE	PHE B:81 , GLU B:82 , ARG B:97 , TRP B:136 , PHE C:81 , GLU C:82 , ARG C:97 , TRP C:136	BINDING SITE FOR RESIDUE SO4 B 165
05	AC5	SOFTWARE	GLU A:56 , GLU A:59 , GLU A:117 , PPV A:163 , NA A:171	BINDING SITE FOR RESIDUE SM A 170
06	AC6	SOFTWARE	GLU B:56 , GLU B:59 , GLU B:60 , GLU B:117	BINDING SITE FOR RESIDUE SM B 170
07	AC7	SOFTWARE	GLU C:56 , GLU C:59 , GLU C:117 , PPV C:163 , NA C:171	BINDING SITE FOR RESIDUE SM C 170
08	AC8	SOFTWARE	THR A:40 , GLU A:56 , GLU A:60 , PPV A:163 , SM A:170	BINDING SITE FOR RESIDUE NA A 171
09	AC9	SOFTWARE	THR C:40 , GLU C:56 , GLU C:60 , GLU C:117 , PPV C:163 , SM C:170	BINDING SITE FOR RESIDUE NA C 171
10	BC1	SOFTWARE	LYS A:7 , ARG A:29 , THR A:40 , GLY A:41 , SO4 A:164 , SM A:170 , NA A:171	BINDING SITE FOR RESIDUE PPV A 163
11	BC2	SOFTWARE	LYS C:7 , ARG C:29 , THR C:40 , GLY C:41 , SM C:170 , NA C:171 , HOH C:183	BINDING SITE FOR RESIDUE PPV C 163

Asymmetric Unit

No.	Residues
1	A:75	-	A:104
2	B:75	-	B:104
3	C:75	-	C:104

(no "Cis Peptide Bond" information available for 2O5W)

(no "SAP(SNP)/Variant" information available for 2O5W)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDB_ECOLI	5-146	2	A:5-146 B:5-146
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDB_ECOLI	41-62	4	A:41-62 B:41-62 C:41-62 D:41-62

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDB_ECOLI	5-146	1	A:5-146 -
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDB_ECOLI	41-62	1	A:41-62 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDB_ECOLI	5-146	1	- B:5-146
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDB_ECOLI	41-62	1	- B:41-62 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDB_ECOLI	5-146	0	- -
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDB_ECOLI	41-62	1	- - C:41-62 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDB_ECOLI	5-146	0	- -
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDB_ECOLI	41-62	1	- - - D:41-62

(no "Exon" information available for 2O5W)

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:147
 aligned with NUDB_ECOLI | P0AFC0 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           NUDB_ECOLI     2 KDKVYKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVIN 148
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee....eeeeee.......ee.eeee.....hhhhhhhhhhhhhhh.........eeeeeeeeeee.hhhhhhhh.....eeeeeeeeeee.............eeeeehhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---NUDIX  PDB: A:5-146 UniProt: 5-146                                                                                                            -- PROSITE (1)
                PROSITE (2) ---------------------------------------NUDIX_BOX  PDB: A:41-6-------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o5w A   2 KDKVYKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVIN 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with NUDB_ECOLI | P0AFC0 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
           NUDB_ECOLI     3 DKVYKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVINA 149
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee....eeeeeee......ee.eeee.....hhhhhhhhhhhhhhh.........eeeeeeeeeee.hhhhhh.......eeeeeeeeeee..........eeeeeeeehhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --NUDIX  PDB: B:5-146 UniProt: 5-146                                                                                                            --- PROSITE (1)
                PROSITE (2) --------------------------------------NUDIX_BOX  PDB: B:41-6--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o5w B   3 DKVYKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVINA 149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with NUDB_ECOLI | P0AFC0 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:142
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145  
           NUDB_ECOLI     6 YKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVI 147
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....eeeee.......ee.eeee.....hhhhhhhhhhhhhhh.hhhhhh..eeeeeeeeeee.hhhhhhhh.....eeeeeeeeeee.............eeeehhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: - UniProt: 5-146                                                                                                                 - PROSITE (1)
                PROSITE (2) -----------------------------------NUDIX_BOX  PDB: C:41-6------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o5w C   6 YKRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVI 147
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

Chain D from PDB  Type:PROTEIN  Length:141
 aligned with NUDB_ECOLI | P0AFC0 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:141
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146 
           NUDB_ECOLI     7 KRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVI 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -NUDIX-2o5wD01 D:8-147                                                                                                                        Pfam domains (1)
           Pfam domains (2) -NUDIX-2o5wD02 D:8-147                                                                                                                        Pfam domains (2)
           Pfam domains (3) -NUDIX-2o5wD03 D:8-147                                                                                                                        Pfam domains (3)
           Pfam domains (4) -NUDIX-2o5wD04 D:8-147                                                                                                                        Pfam domains (4)
         Sec.struct. author ...eeeeeeeee....eeeeee.......ee.eeee.....hhhhhhhhhhhhhhh...............eeeee..............eeeeeeeeeee.............eeeeehhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: - UniProt: 5-146                                                                                                                - PROSITE (1)
                PROSITE (2) ----------------------------------NUDIX_BOX  PDB: D:41-6------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o5w D   7 KRPVSILVVIYAQDTKRVLMLQRRDDPDFWQSVTGSVEEGETAPQAAMREVKEEVTIDVVAEQLTLIDCQRTVEFEIFSHLRHRYAPGVTRNTESWFCLALPHERQIVFTEHLAYKWLDAPAAAALTKSWSNRQAIEQFVI 147
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 2O5W)

(no "CATH Domain" information available for 2O5W)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-2o5wD01	D:8-147
1b	NUDIX-2o5wD02	D:8-147
1c	NUDIX-2o5wD03	D:8-147
1d	NUDIX-2o5wD04	D:8-147

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NUDB_ECOLI | P0AFC0)

molecular function
	GO:0008828	dATP pyrophosphohydrolase activity	Catalysis of the reaction: deoxy-ATP + H2O = dAMP + diphosphate.
	GO:0019177	dihydroneopterin triphosphate pyrophosphohydrolase activity	Catalysis of the reaction: dihydroneopterin triphosphate = dihydroneopterin phosphate + diphosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0046656	folic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
	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.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (4, 11)

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