1VC9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A T.THERMOPHILUS HB8 AP6A HYDROLASE E50Q MUTANT-MG2+-ATP COMPLEX

Authors :   T. Iwai, N. Nakagawa, S. Kuramitsu, R. Masui, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   05 Mar 04 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Nudix Protein, Diadenosine Polyphosphate, Ap6A, Thermus Thermophilus Hb8, Hydrolase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Iwai, N. Nakagawa, S. Kuramitsu, R. Masui
Crystal Structure Of Nudix Protein Ndx1 From Thermus Thermophilus Hb8 In Binary Complex With Diadenosine Hexaphosphate
To Be Published
PubMed: search

Molecule 1 - NDX1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NDX1
	Mutation	:	YES
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	MUTT/NUDIX FAMILY PROTEIN

		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, 3)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:32 , GLU A:46 , HOH A:2010 , HOH A:2060	BINDING SITE FOR RESIDUE MG A 2001
2	AC2	SOFTWARE	ASP A:21 , MET A:23 , PHE A:25 , LYS A:30 , HIS A:32 , TYR A:66 , ASN A:68 , PRO A:69 , ARG A:74 , PHE A:110 , GLU A:112 , HOH A:2002 , HOH A:2005 , HOH A:2012 , HOH A:2048	BINDING SITE FOR RESIDUE ATP A 1001
3	AC3	SOFTWARE	ASP B:21 , MET B:23 , PHE B:25 , LYS B:30 , HIS B:32 , TYR B:66 , ASN B:68 , PRO B:69 , ARG B:74 , PHE B:110 , GLU B:112 , HOH B:1003 , HOH B:1011 , HOH B:1023 , HOH B:1037 , HOH B:1045	BINDING SITE FOR RESIDUE ATP B 1002

(no "SS Bond" information available for 1VC9)

(no "Cis Peptide Bond" information available for 1VC9)

(no "SAP(SNP)/Variant" information available for 1VC9)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NDX1_THETH	1-121	2	A:1-121 B:1-121
2	NUDIX_BOX	PS00893	Nudix box signature.	NDX1_THETH	31-52	2	A:31-52 B:31-52

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NDX1_THETH	1-121	1	A:1-121 -
2	NUDIX_BOX	PS00893	Nudix box signature.	NDX1_THETH	31-52	1	A:31-52 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NDX1_THETH	1-121	1	- B:1-121
2	NUDIX_BOX	PS00893	Nudix box signature.	NDX1_THETH	31-52	1	- B:31-52

(no "Exon" information available for 1VC9)

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:126
 aligned with NDX1_THETH | Q75UV1 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           NDX1_THETH     1 MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEETGVRAEVLLPLYPTRYVNPKGVEREVHWFLMRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL 126
               SCOP domains d1vc9a1 A:1-126 AP6A hydrolase Ndx1                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeeee.....ee..ee......hhhhhhhhhhhhhhh...eeeee...eeee.....eeeeeeeeee............eeeeehhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: A:1-121 UniProt: 1-121                                                                                       ----- PROSITE (1)
                PROSITE (2) ------------------------------NUDIX_BOX  PDB: A:31-5-------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vc9 A   1 MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEQTGVRAEVLLPLYPTRYVNPKGVEREVHWFLMRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with NDX1_THETH | Q75UV1 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           NDX1_THETH     1 MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEETGVRAEVLLPLYPTRYVNPKGVEREVHWFLMRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL 126
               SCOP domains d1vc9b_ B: AP6A hydrolase Ndx1                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeeee.....ee..ee......hhhhhhhhhhhhhhh.eeeeeeeeeeeeee.....eeeeeeeeeeee..........eeeeehhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: B:1-121 UniProt: 1-121                                                                                       ----- PROSITE (1)
                PROSITE (2) ------------------------------NUDIX_BOX  PDB: B:31-5-------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vc9 B   1 MELGAGGVVFNAKREVLLLRDRMGFWVFPKGHPEPGESLEEAAVREVWEQTGVRAEVLLPLYPTRYVNPKGVEREVHWFLMRGEGAPRLEEGMTGAGWFSPEEARALLAFPEDLGLLEVALERLPL 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

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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 '\|'

Asymmetric Unit

Classes(

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: MutT-like (82)

Protein domain: AP6A hydrolase Ndx1 (3)

Thermus thermophilus [TaxId: 274] (3)

1a	d1vc9a1	A:1-126
1b	d1vc9b_	B:

(no "CATH Domain" information available for 1VC9)

(no "Pfam Domain" information available for 1VC9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NDX1_THETH | Q75UV1)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

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	1vc9
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UniProtKB/Swiss-Prot
	NDX1_THETH \| Q75UV1	:	1vc8 1vcd

1vc8	T.THERMOPHILUS HB8 AP6A HYDROLASE NDX1-AP6A COMPLEX
1vcd	T.THERMOPHILUS HB8 AP6A HYDROLASE NDX1 RELATED ID: TTK003001331.5 RELATED DB: TARGETDB

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