1XQI - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF AN NDP KINASE FROM PYROBACULUM AEROPHILUM

Authors :   J. D. Pedelacq, G. S. Waldo, S. Cabantous, E. C. Liong, J. Berendzen, T. C. Terwilliger

Date :   12 Oct 04 (Deposition) - 20 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha/Beta Sandwich, Ferredoxin Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Pedelacq, G. S. Waldo, S. Cabantous, E. C. Liong, T. C. Terwilliger
Structural And Functional Features Of An Ndp Kinase From The Hyperthermophile Crenarchaeon Pyrobaculum Aerophilum
Protein Sci. V. 14 2562 2005
PubMed-ID: 16195547 | Reference-DOI: 10.1110/PS.051664205
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET 28 C-6HIS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK
	Mutation	:	YES
	Organism Scientific	:	PYROBACULUM AEROPHILUM
	Organism Taxid	:	13773
	Strain	:	STRAIN IM2 DSM 7523 ATCC 51768
	Synonym	:	NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL
3	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MSE	-1	Mod. Amino Acid	SELENOMETHIONINE
2	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
3	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:23 , TYR A:63 , ASN A:169 , HIS A:172 , PGE A:500	BINDING SITE FOR RESIDUE TRS A 200
2	AC2	SOFTWARE	LYS B:23 , TYR B:63 , THR B:138 , ASN B:169 , VAL B:171 , HIS B:172 , PGE B:600 , HOH B:613	BINDING SITE FOR RESIDUE TRS B 300
3	AC3	SOFTWARE	LYS C:23 , TYR C:63 , THR C:138 , ASN C:169 , HIS C:172 , PGE C:700 , HOH C:730 , HOH C:755	BINDING SITE FOR RESIDUE TRS C 400
4	AC4	SOFTWARE	TYR A:63 , PRO A:64 , TRP A:69 , HIS A:172 , ALA A:173 , SER A:174 , ASP A:175 , GLU A:179 , GLU A:183 , TRS A:200 , HOH A:505	BINDING SITE FOR RESIDUE PGE A 500
5	AC5	SOFTWARE	TYR B:63 , PRO B:64 , TRP B:69 , HIS B:172 , ALA B:173 , SER B:174 , ASP B:175 , GLU B:179 , GLU B:183 , TRS B:300 , HOH B:653	BINDING SITE FOR RESIDUE PGE B 600
6	AC6	SOFTWARE	TYR C:63 , PRO C:64 , TRP C:69 , HIS C:172 , ALA C:173 , SER C:174 , ASP C:175 , GLU C:179 , GLU C:183 , TRS C:400 , HOH C:749	BINDING SITE FOR RESIDUE PGE C 700

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_PYRAE	157-165	3	A:169-177 B:169-177 C:169-177

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_PYRAE	157-165	2	A:169-177 - C:169-177

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_PYRAE	157-165	2	- B:169-177 -

Biological Unit 3 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_PYRAE	157-165	6	A:169-177 B:169-177 C:169-177

(no "Exon" information available for 1XQI)

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:182
 aligned with NDK_PYRAE | Q8ZWY4 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
            NDK_PYRAE     2 PVEKTLLILKPDAVARGLVGEIISRFEKAGLKIVALKMVKASPEEIERFYPSSEEWLRSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRSLVKYMTSGPIVVMVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 183
               SCOP domains d1xqia1 A:14-195 Nucleoside diphosphate kinase, NDK                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhh.......eee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xqi A  14 PVEKTLLILKPDAVARGLVDEIISRFKKAGLKIVALKmVKASPEEIERFYPSSEEWLQSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRNLVKYmTSGPNVVmVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 195
                                    23        33        43       |53        63        73        83        93       103       113      |123       133       143       153       163       173       183       193  
                                                                51-MSE                                                      112-MSE 120-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with NDK_PYRAE | Q8ZWY4 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
            NDK_PYRAE     2 PVEKTLLILKPDAVARGLVGEIISRFEKAGLKIVALKMVKASPEEIERFYPSSEEWLRSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRSLVKYMTSGPIVVMVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 183
               SCOP domains d1xqib_ B: Nucleoside diphosphate kinase, NDK                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhh.......eee..hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xqi B  14 PVEKTLLILKPDAVARGLVDEIISRFKKAGLKIVALKmVKASPEEIERFYPSSEEWLQSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRNLVKYmTSGPNVVmVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 195
                                    23        33        43       |53        63        73        83        93       103       113      |123       133       143       153       163       173       183       193  
                                                                51-MSE                                                      112-MSE 120-MSE

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with NDK_PYRAE | Q8ZWY4 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
            NDK_PYRAE     2 PVEKTLLILKPDAVARGLVGEIISRFEKAGLKIVALKMVKASPEEIERFYPSSEEWLRSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRSLVKYMTSGPIVVMVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 183
               SCOP domains d1xqic_ C: Nucleoside diphosphate kinase, NDK                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------NDK-1xqiC01 C:98-193                                                                            -- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------NDK-1xqiC02 C:98-193                                                                            -- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------NDK-1xqiC03 C:98-193                                                                            -- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------NDK-1xqiC04 C:98-193                                                                            -- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------NDK-1xqiC05 C:98-193                                                                            -- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------NDK-1xqiC06 C:98-193                                                                            -- Pfam domains (6)
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhh.......eee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xqi C  14 PVEKTLLILKPDAVARGLVDEIISRFKKAGLKIVALKmVKASPEEIERFYPSSEEWLQSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRNLVKYmTSGPNVVmVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE 195
                                    23        33        43       |53        63        73        83        93       103       113      |123       133       143       153       163       173       183       193  
                                                                51-MSE                                                      112-MSE 120-MSE

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)

Pyrobaculum aerophilum [TaxId: 13773] (1)

1a	d1xqia1	A:14-195
1b	d1xqib_	B:
1c	d1xqic_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NDK] (40)

Family: NDK (40)

Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) (1)

1a	NDK-1xqiC01	C:98-193
1b	NDK-1xqiC02	C:98-193
1c	NDK-1xqiC03	C:98-193
1d	NDK-1xqiC04	C:98-193
1e	NDK-1xqiC05	C:98-193
1f	NDK-1xqiC06	C:98-193

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NDK_PYRAE | Q8ZWY4)

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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	1xqi
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1npk	THE SAME PROTEIN FROM DICTYOSTELIUM DISCOIDEUM

Description

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Ligands, Modified Residues, Ions (3, 15)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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