2XJD - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH INORGANIC PHOSPHATE AND DEOXYADENOSINE TRIPHOSPHATE

Authors :   K. Wallden, P. Nordlund

Date :   04 Jul 10 (Deposition) - 27 Apr 11 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Allosteric Enzyme, Cn-Ii, Gmp-Imp Specific Nucleotidase, High Km 5-Prime Nucleotidase, Hydrolase, Metal-Binding, Nt5C2, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wallden, P. Nordlund
Structural Basis For The Allosteric Regulation And Substrate Recognition Of Human Cytosolic 5'-Nucleotidase Ii
J. Mol. Biol. V. 408 684 2011
PubMed-ID: 21396942 | Reference-DOI: 10.1016/J.JMB.2011.02.059
(for further references see the PDB file header)

Molecule 1 - CYTOSOLIC PURINE 5'-NUCLEOTIDASE
	Chains	:	A
	EC Number	:	3.1.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector	:	P28A-LIC
	Fragment	:	RESIDUES 1-536
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYTOSOLIC 5'-NUCLEOTIDASE II

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	6	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	12	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:144 , ASP A:145 , ASN A:154 , PHE A:354 , LYS A:362 , GLN A:453 , ARG A:456 , TYR A:457 , MG A:1498 , HOH A:2175 , HOH A:2176 , HOH A:2381 , HOH A:2382 , HOH A:2438 , HOH A:2439 , HOH A:2440 , HOH A:2441 , HOH A:2442 , HOH A:2443 , HOH A:2444	BINDING SITE FOR RESIDUE ATP A1489
02	AC2	SOFTWARE	HIS A:209 , TYR A:210 , LYS A:215 , SER A:251 , TYR A:255 , GOL A:1493 , HOH A:2445	BINDING SITE FOR RESIDUE GOL A1490
03	AC3	SOFTWARE	PHE A:283 , ASP A:284 , ILE A:286 , LEU A:321 , GLN A:322 , HIS A:323 , GLY A:324 , ILE A:325 , HOH A:2353 , HOH A:2446 , HOH A:2447	BINDING SITE FOR RESIDUE GOL A1491
04	AC4	SOFTWARE	PHE A:198 , GLN A:199 , ARG A:202 , HOH A:2188 , HOH A:2231 , HOH A:2449	BINDING SITE FOR RESIDUE GOL A1492
05	AC5	SOFTWARE	PHE A:157 , ARG A:202 , VAL A:205 , ASP A:206 , TYR A:210 , GOL A:1490	BINDING SITE FOR RESIDUE GOL A1493
06	AC6	SOFTWARE	PRO A:96 , GLU A:374 , GLU A:378 , TYR A:434 , HOH A:2391 , HOH A:2451 , HOH A:2453 , HOH A:2454 , HOH A:2455	BINDING SITE FOR RESIDUE GOL A1494
07	AC7	SOFTWARE	ASP A:257 , THR A:261 , PRO A:278 , TRP A:279 , GLN A:280 , HOH A:2456 , HOH A:2457	BINDING SITE FOR RESIDUE GOL A1495
08	AC8	SOFTWARE	ASN A:52 , MET A:53 , ASP A:54 , THR A:249 , ASN A:250 , SER A:251 , LYS A:292 , MG A:1497 , HOH A:2372 , HOH A:2374 , HOH A:2445 , HOH A:2458	BINDING SITE FOR RESIDUE PO4 A1496
09	AC9	SOFTWARE	ASN A:52 , ASP A:54 , ASP A:351 , PO4 A:1496 , HOH A:2372 , HOH A:2374	BINDING SITE FOR RESIDUE MG A1497
10	BC1	SOFTWARE	LYS A:362 , ATP A:1489 , HOH A:2381	BINDING SITE FOR RESIDUE MG A1498

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

Asymmetric Unit

No.	Residues
1	Ser A:62	-	Pro A:63
2	Lys A:292	-	Pro A:293

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024244	T	3	A	5NTC_HUMAN	Polymorphism	10883841	A	T	3	A
2	UniProt	VAR_030242	Q	136	R	5NTC_HUMAN	Polymorphism	12262171	A	Q	136	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024244	T	3	A	5NTC_HUMAN	Polymorphism	10883841	A	T	3	A
2	UniProt	VAR_030242	Q	136	R	5NTC_HUMAN	Polymorphism	12262171	A	Q	136	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2XJD)

Asymmetric Unit (17, 17)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000343289	1a	ENSE00001759705	chr10:104953056-104952993	64	5NTC_HUMAN	-	0	0	-	-
1.3	ENST00000343289	3	ENSE00002186305	chr10:104934739-104934615	125	5NTC_HUMAN	1-34	34	1	A:3-34	32
1.6	ENST00000343289	6	ENSE00001787725	chr10:104899236-104899163	74	5NTC_HUMAN	34-59	26	1	A:34-59	26
1.8a	ENST00000343289	8a	ENSE00001707803	chr10:104866463-104866346	118	5NTC_HUMAN	59-98	40	1	A:59-98	40
1.9a	ENST00000343289	9a	ENSE00001645482	chr10:104865558-104865463	96	5NTC_HUMAN	98-130	33	1	A:98-130	33
1.11	ENST00000343289	11	ENSE00001742963	chr10:104861083-104860992	92	5NTC_HUMAN	130-161	32	1	A:130-161	32
1.12	ENST00000343289	12	ENSE00001739246	chr10:104860859-104860802	58	5NTC_HUMAN	161-180	20	1	A:161-180	20
1.15	ENST00000343289	15	ENSE00001753876	chr10:104859776-104859683	94	5NTC_HUMAN	180-211	32	1	A:180-211	32
1.16a	ENST00000343289	16a	ENSE00001705007	chr10:104858741-104858688	54	5NTC_HUMAN	212-229	18	1	A:212-229	18
1.18b	ENST00000343289	18b	ENSE00002152144	chr10:104857131-104857048	84	5NTC_HUMAN	230-257	28	1	A:230-257	28
1.19	ENST00000343289	19	ENSE00001748493	chr10:104855737-104855696	42	5NTC_HUMAN	258-271	14	1	A:258-271	14
1.20b	ENST00000343289	20b	ENSE00001646238	chr10:104854212-104854105	108	5NTC_HUMAN	272-307	36	1	A:272-307	36
1.21a	ENST00000343289	21a	ENSE00001596497	chr10:104853795-104853729	67	5NTC_HUMAN	308-330	23	1	A:308-330	23
1.22	ENST00000343289	22	ENSE00001711453	chr10:104853066-104852896	171	5NTC_HUMAN	330-387	58	1	A:330-387	58
1.23	ENST00000343289	23	ENSE00001659728	chr10:104851372-104851321	52	5NTC_HUMAN	387-404	18	1	A:387-395	9
1.24	ENST00000343289	24	ENSE00001610324	chr10:104850753-104850693	61	5NTC_HUMAN	404-424	21	1	A:420-424	5
1.25	ENST00000343289	25	ENSE00001778811	chr10:104850544-104850368	177	5NTC_HUMAN	425-483	59	1	A:425-483	59
1.26d	ENST00000343289	26d	ENSE00001648268	chr10:104849665-104845940	3726	5NTC_HUMAN	484-561	78	1	A:484-488	5

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:462
 aligned with 5NTC_HUMAN | P49902 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:486
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482      
           5NTC_HUMAN     3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 488
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------5_nucleotid-2xjdA01 A:35-488                                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.ee...ee.hhh.eeee...........hhhhhhhhhhhhhhhhhh..hhhhhhh...........eee....eeeee.....eeeeee..ee.hhhhhh...............eee..hhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhheeeee...hhhhhhhhhhhhh.............hhhhhh.eeee....hhhhh....eee......................eee.hhhhhhhhhh.hhh.eeeee.....hhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhh------------------------hhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhhh....ee......hhhhh Sec.struct. author
                 SAPs(SNPs) A------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:3-34           ------------------------Exon 1.8a  PDB: A:59-98 UniProt: 59-98  -------------------------------Exon 1.11  PDB: A:130-161       ------------------Exon 1.15  PDB: A:180-211       Exon 1.16a        Exon 1.18b  PDB: A:230-257  Exon 1.19     Exon 1.20b  PDB: A:272-307          Exon 1.21a             --------------------------------------------------------Exon 1.23         --------------------Exon 1.25  PDB: A:425-483 UniProt: 425-483                 1.26d Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.6  PDB: A:34-59    --------------------------------------Exon 1.9a  PDB: A:98-130         ------------------------------Exon 1.12           -----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.22  PDB: A:330-387 UniProt: 330-387                ----------------Exon 1.24            ---------------------------------------------------------------- Transcript 1 (2)
                 2xjd A   3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFNMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSL------------------------QRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 488
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392  |      -         -       422       432       442       452       462       472       482      
                                                                                                                                                                                                                                                                                                                                                                                                                                  395                      420

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 2XJD)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: 5_nucleotid (10)

Homo sapiens (Human) (10)

5_nucleotid-2xjdA01

A:35-488

Asymmetric Unit(hide GO term definitions)

Chain A (5NTC_HUMAN | P49902)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0050146	nucleoside phosphotransferase activity	Catalysis of the reaction: a nucleotide + a 2'-deoxynucleoside = a nucleoside + a 2'-deoxynucleoside 5'-monophosphate.
	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).
biological process
	GO:0046040	IMP metabolic process	The chemical reactions and pathways involving IMP, inosine monophosphate.
	GO:0046085	adenosine metabolic process	The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0017144	drug metabolic process	The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0006195	purine nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of 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.
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.

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		Lys A:292 - Pro A:293	[ RasMol ]
		Ser A:62 - Pro A:63	[ RasMol ]

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2j2c	CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II (NT5C2, CN-II)
2jc9	CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II IN COMPLEX WITH ADENOSINE
2jcm	CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II IN COMPLEX WITH BERYLLIUM TRIFLUORIDE
2xcv	CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND 2,3- BISPHOSPHOGLYCERATE
2xjb	CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH DEOXYGUANOSINE MONOPHOSPHATE AND DEOXYADENOSINE TRIPHOSPHATE
2xjc	CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH GUANOSINE MONOPHOSPHATE AND DIADENOSINE TETRAPHOSPHATE
2xje	CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE AND ADENOSINE TRIPHOSPHATE
2xjf	CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II WITH A COVALENTLY MODIFIED ASN52

Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (17, 17)

Sequences/Alignments

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Pfam Domains (1, 1)

Gene Ontology (17, 17)

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