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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCUTRE OF DELETION MUTANT OF APS-KINASE DOMAIN OF HUMAN PAPS-SYNTHETASE 1

Authors :   N. Sekulic, A. Lavie

Date :   03 Apr 07 (Deposition) - 29 May 07 (Release) - 13 May 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Nucleic Acid Complex, Nmp-Kinase Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sekulic, M. Konrad, A. Lavie
Structural Mechanism For Substrate Inhibition Of The Adenosine 5'-Phosphosulfate Kinase Domain Of Human 3'-Phosphoadenosine 5'-Phosphosulfate Synthetase 1 And Its Ramifications For Enzyme Regulation.
J. Biol. Chem. V. 282 22112 2007
PubMed-ID: 17540769 | Reference-DOI: 10.1074/JBC.M701713200
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'- PHOSPHOSULFATE SYNTHETASE 1 (PAPS SYNTHETASE 1) (PAPSS 1) (SULFURYLASE KINASE 1) (SK1) (SK 1)
	Chains	:	A, B
	EC Number	:	2.7.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-RB IN WHICH THE THROMBIN SITE WAS REPLACED BY TEV CUTTING SITE
	Expression System Strain	:	BL-21 CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	APS-KINASE DOMAIN (RESIDUES 51-226)
	Gene	:	PAPSS1, ATPSK1, PAPSS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ADX	1	Ligand/Ion	ADENOSINE-5'-PHOSPHOSULFATE
2	DAT	2	Ligand/Ion	2'-DEOXYADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:92 , PHE A:101 , ARG A:106 , ASN A:109 , PHE A:131 , ILE A:132 , SER A:133 , PRO A:134 , LEU A:173 , GLY A:184 , PHE A:185 , THR A:186 , HOH A:414 , HOH A:419 , HOH A:444 , HOH A:459	BINDING SITE FOR RESIDUE ADX A 400
2	AC2	SOFTWARE	LEU A:60 , GLY A:62 , ALA A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , ARG A:168 , THR A:204 , CYS A:207 , ASP A:208 , VAL A:209 , HOH A:414 , HOH A:432 , HOH A:443 , HOH A:452 , HIS B:163 , GLN B:167	BINDING SITE FOR RESIDUE DAT A 300
3	AC3	SOFTWARE	HIS A:163 , GLN A:167 , LEU B:60 , GLY B:62 , ALA B:63 , GLY B:64 , LYS B:65 , THR B:66 , THR B:67 , VAL B:68 , ARG B:168 , VAL B:170 , THR B:204 , CYS B:207 , ASP B:208 , VAL B:209 , HOH B:251 , HOH B:263 , HOH B:277	BINDING SITE FOR RESIDUE DAT B 227

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

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

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

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

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000265174	1a	ENSE00000935008	chr4:108641608-108641276	333	PAPS1_HUMAN	1-20	20	0	-	-
1.3	ENST00000265174	3	ENSE00000935007	chr4:108622441-108622327	115	PAPS1_HUMAN	21-59	39	2	A:51-59 B:51-59	9 9
1.4c	ENST00000265174	4c	ENSE00000736237	chr4:108615162-108614927	236	PAPS1_HUMAN	59-137	79	2	A:59-137 B:59-137	79 79
1.5c	ENST00000265174	5c	ENSE00000736234	chr4:108608333-108608195	139	PAPS1_HUMAN	138-184	47	2	A:138-184 B:138-170	47 33
1.6	ENST00000265174	6	ENSE00000736231	chr4:108603289-108603171	119	PAPS1_HUMAN	184-223	40	2	A:184-223 B:191-223	40 33
1.7b	ENST00000265174	7b	ENSE00000841651	chr4:108581228-108581115	114	PAPS1_HUMAN	224-261	38	2	A:224-226 B:224-226	3 3
1.8	ENST00000265174	8	ENSE00000841650	chr4:108578163-108578052	112	PAPS1_HUMAN	262-299	38	0	-	-
1.9	ENST00000265174	9	ENSE00000841649	chr4:108576056-108575851	206	PAPS1_HUMAN	299-367	69	0	-	-
1.10b	ENST00000265174	10b	ENSE00001217423	chr4:108574782-108574647	136	PAPS1_HUMAN	368-413	46	0	-	-
1.11	ENST00000265174	11	ENSE00001217417	chr4:108566226-108565958	269	PAPS1_HUMAN	413-502	90	0	-	-
1.12a	ENST00000265174	12a	ENSE00001217412	chr4:108553016-108552787	230	PAPS1_HUMAN	503-579	77	0	-	-
1.13	ENST00000265174	13	ENSE00001217468	chr4:108535543-108534822	722	PAPS1_HUMAN	579-624	46	0	-	-

Asymmetric/Biological 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:176
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:176
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
          PAPS1_HUMAN    51 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIV 226
               SCOP domains d2peya_ A: automated matches                                                                                                                                                     SCOP domains
               CATH domains 2peyA00 A:51-226 P-loop containing nucleotide triphosphate hydrolases                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh..hhhhhhhh....................eee.....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3 ------------------------------------------------------------------------------Exon 1.5c  PDB: A:138-184 UniProt: 138-184     ---------------------------------------1.7 Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.4c  PDB: A:59-137 UniProt: 59-137                                       ----------------------------------------------Exon 1.6  PDB: A:184-223                --- Transcript 1 (2)
                 2pey A  51 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIV 226
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:176
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
          PAPS1_HUMAN    51 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIV 226
               SCOP domains d2peyb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) APS_kinase-2peyB01 B:51-209                                                                                                                                    ----------------- Pfam domains (1)
           Pfam domains (2) APS_kinase-2peyB02 B:51-209                                                                                                                                    ----------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhh.--------------------.........eeee....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3 ------------------------------------------------------------------------------Exon 1.5c  PDB: B:138-170 UniProt: 138-184     ---------------------------------------1.7 Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.4c  PDB: B:59-137 UniProt: 59-137                                       ----------------------------------------------Exon 1.6  PDB: B:191-223 [INCOMPLETE]   --- Transcript 1 (2)
                 2pey B  51 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDV--------------------EYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIV 226
                                    60        70        80        90       100       110       120       130       140       150       160       170         -         -|      200       210       220      
                                                                                                                                                 170                  191

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Adenosine-5'phosphosulfate kinase (APS kinase) (9)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2peya_	A:
1b	d2peyb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

2peyA00

A:51-226

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: APS_kinase (10)

Homo sapiens (Human) (7)

1a	APS_kinase-2peyB01	B:51-209
1b	APS_kinase-2peyB02	B:51-209

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PAPS1_HUMAN | O43252)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004020	adenylylsulfate kinase activity	Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
	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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004781	sulfate adenylyltransferase (ATP) activity	Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate.
	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:0050428	3'-phosphoadenosine 5'-phosphosulfate biosynthetic process	The chemical reactions and pathways resulting in the formation of 3'-phosphoadenosine 5'-phosphosulfate, a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.
	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: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:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
	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/Biological Unit
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	2pey
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	2.7.1.25
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	PAPS1_HUMAN \| O43252	:	1x6v 1xjq 1xnj 2ofw 2ofx 2pez 2qjf

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (5, 10)

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