2HUR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   ESCHERICHIA COLI NUCLEOSIDE DIPHOSPHATE KINASE

Authors :   L. Moynie, M. -F. Giraud, F. Georgescauld, I. Lascu, A. Dautant

Date :   27 Jul 06 (Deposition) - 10 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F  (2x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: E,F  (1x)
Biol. Unit 5: C,D  (1x)

Keywords :   Type Ii Tetramer, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Moynie, M. -F. Giraud, F. Georgescauld, I. Lascu, A. Dautant
The Structure Of The Escherichia Coli Nucleoside Diphosphat Kinase Reveals A New Quaternary Architecture For This Enzym Family
Proteins V. 67 755 2007
PubMed-ID: 17330300 | Reference-DOI: 10.1002/PROT.21316
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJC20
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NDK; NDP KINASE; NUCLEOSIDE-2-P KINASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:					E	F
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:					E	F
Biological Unit 5 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:11 , THR A:93 , ARG A:104 , ASN A:114 , HIS A:117 , HOH A:226 , HOH A:237 , HOH A:264	BINDING SITE FOR RESIDUE SO4 A 200
2	AC2	SOFTWARE	LYS B:11 , THR B:93 , ARG B:104 , ASN B:114 , HIS B:117 , HOH B:246 , HOH B:276 , HOH B:322	BINDING SITE FOR RESIDUE SO4 B 200
3	AC3	SOFTWARE	LYS C:11 , THR C:93 , ARG C:104 , ASN C:114 , HIS C:117 , HOH C:247 , HOH C:258	BINDING SITE FOR RESIDUE SO4 C 200
4	AC4	SOFTWARE	LYS D:11 , THR D:93 , ARG D:104 , ASN D:114 , HIS D:117 , HOH D:327 , HOH D:334 , HOH D:397 , HOH D:408 , HOH D:443 , HOH F:360	BINDING SITE FOR RESIDUE SO4 D 200
5	AC5	SOFTWARE	LYS E:11 , THR E:93 , ARG E:104 , ASN E:114 , HIS E:117 , HOH E:287	BINDING SITE FOR RESIDUE SO4 E 200
6	AC6	SOFTWARE	HOH D:343 , LYS F:11 , THR F:93 , ARG F:104 , ASN F:114 , HIS F:117 , HOH F:290 , HOH F:302 , HOH F:329 , HOH F:332 , HOH F:344	BINDING SITE FOR RESIDUE SO4 F 200

(no "SS Bond" information available for 2HUR)

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

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	6	A:114-122 B:114-122 C:114-122 D:114-122 E:114-122 F:114-122

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	4	A:114-122 B:114-122 C:114-122 D:114-122 - -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	4	- - - - E:114-122 F:114-122

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	2	A:114-122 B:114-122 - - - -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	2	- - - - E:114-122 F:114-122

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_ECOLI	114-122	2	- - C:114-122 D:114-122 - -

(no "Exon" information available for 2HUR)

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:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hura_ A: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur A   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hurb_ B: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur B   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hurc_ C: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur C   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hurd_ D: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur D   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain E from PDB  Type:PROTEIN  Length:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hure_ E: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur E   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain F from PDB  Type:PROTEIN  Length:142
 aligned with NDK_ECOLI | P0A763 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            NDK_ECOLI     2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
               SCOP domains d2hurf_ F: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hur F   2 AIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ferredoxin-like (1795)

Superfamily: Nucleoside diphosphate kinase, NDK (129)

Family: Nucleoside diphosphate kinase, NDK (112)

Protein domain: Nucleoside diphosphate kinase, NDK (66)

Escherichia coli [TaxId: 562] (1)

1a	d2hura_	A:
1b	d2hurb_	B:
1c	d2hurc_	C:
1d	d2hurd_	D:
1e	d2hure_	E:
1f	d2hurf_	F:

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

(no "Pfam Domain" information available for 2HUR)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (NDK_ECOLI | P0A763)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006241	CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
	GO:0006183	GTP biosynthetic process	The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
	GO:0006228	UTP biosynthetic process	The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009142	nucleoside triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hur)

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	2hur
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1npk	REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE DIPHOSPHATE KINASE AT 1.8 ANGSTROMS RESOLUTION
2nck	CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS

Description

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Ligands, Modified Residues, Ions (1, 6)

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