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Title :   CRYSTAL STRUCTURE OF THE APSK DOMAIN OF HUMAN PAPSS1 IN COMPLEX WITH ADPMG AND PAPS

Authors :   N. Sekulic, A. Lavie

Date :   04 Jan 07 (Deposition) - 10 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Nucleotide Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sekulic, K. Dietrich, I. Paarmann, S. Ort, M. Konrad, A. Lavie
Elucidation Of The Active Conformation Of The Aps-Kinase Domain Of Human Paps Synthetase 1.
J. Mol. Biol. V. 367 488 2007
PubMed-ID: 17276460 | Reference-DOI: 10.1016/J.JMB.2007.01.025
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'- PHOSPHOSULFATE SYNTHETASE 1
	Chains	:	A, B
	EC Number	:	2.7.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-RB WITH ENGINEERED TEV CUTTING SITE
	Expression System Strain	:	BL-21 CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	APS KINASE DOMAIN (RESIDUES 1-227)
	Gene	:	PAPSS1
	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 (4, 10)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	PO4	4	Ligand/Ion	PHOSPHATE ION
4	PPS	2	Ligand/Ion	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:66 , PPS A:1100 , ADP A:1300 , HOH A:1327 , HOH A:1358 , HOH A:1363	BINDING SITE FOR RESIDUE MG A 301
02	AC2	SOFTWARE	THR B:66 , ASP B:87 , PPS B:1200 , ADP B:1400 , HOH B:1410 , HOH B:1438 , HOH B:1460	BINDING SITE FOR RESIDUE MG B 302
03	AC3	SOFTWARE	ARG A:139 , ASN A:140 , GLU A:155 , PRO A:195 , GLU A:196 , ALA A:197 , PRO A:198 , HOH A:1365	BINDING SITE FOR RESIDUE PO4 A 401
04	AC4	SOFTWARE	ARG B:139 , ASN B:140 , GLU B:155 , PRO B:195 , GLU B:196 , ALA B:197 , PRO B:198 , HOH B:1449 , HOH B:1497	BINDING SITE FOR RESIDUE PO4 B 402
05	AC5	SOFTWARE	PRO A:161 , HIS A:163 , TYR B:75 , HIS B:79 , GLN B:214	BINDING SITE FOR RESIDUE PO4 A 403
06	AC6	SOFTWARE	TYR A:75 , HIS A:79 , GLN A:214 , PRO B:161 , HIS B:163	BINDING SITE FOR RESIDUE PO4 B 404
07	AC7	SOFTWARE	SER A:61 , LYS A:65 , GLY A:88 , ASP A:89 , ARG A:92 , PHE A:101 , ARG A:106 , ASN A:109 , PHE A:131 , ILE A:132 , SER A:133 , PRO A:134 , LYS A:171 , LEU A:173 , LYS A:183 , GLY A:184 , PHE A:185 , THR A:186 , MG A:301 , ADP A:1300 , HOH A:1327 , HOH A:1329 , HOH A:1339 , HOH A:1358 , HOH A:1363 , THR B:26 , ASN B:27 , VAL B:28 , HOH B:1407 , HOH B:1452	BINDING SITE FOR RESIDUE PPS A 1100
08	AC8	SOFTWARE	THR A:26 , ASN A:27 , VAL A:28 , HOH A:1351 , SER B:61 , LYS B:65 , GLY B:88 , ASP B:89 , ARG B:92 , PHE B:101 , ARG B:106 , ASN B:109 , PHE B:131 , ILE B:132 , SER B:133 , PRO B:134 , LYS B:171 , LEU B:173 , LYS B:183 , GLY B:184 , PHE B:185 , THR B:186 , MG B:302 , ADP B:1400 , HOH B:1417 , HOH B:1432 , HOH B:1438 , HOH B:1458 , HOH B:1459 , HOH B:1460	BINDING SITE FOR RESIDUE PPS B 1200
09	AC9	SOFTWARE	LEU A:60 , GLY A:62 , ALA A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , VAL A:68 , ARG A:168 , VAL A:170 , THR A:204 , CYS A:207 , ASP A:208 , VAL A:209 , CYS A:212 , MG A:301 , PPS A:1100 , HOH A:1327 , HOH A:1343 , HOH A:1358 , HOH A:1373	BINDING SITE FOR RESIDUE ADP A 1300
10	BC1	SOFTWARE	LEU B:60 , SER B:61 , 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 , CYS B:212 , MG B:302 , PPS B:1200 , HOH B:1410 , HOH B:1438 , HOH B:1457 , HOH B:1458 , HOH B:1478 , HOH B:1495	BINDING SITE FOR RESIDUE ADP B 1400

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

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

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

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

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:23-59 B:23-59	37 37
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:138-184	47 47
1.6	ENST00000265174	6	ENSE00000736231	chr4:108603289-108603171	119	PAPS1_HUMAN	184-223	40	2	A:184-223 B:184-223	40 40
1.7b	ENST00000265174	7b	ENSE00000841651	chr4:108581228-108581115	114	PAPS1_HUMAN	224-261	38	2	A:224-227 B:224-227	4 4
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
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Chain A from PDB  Type:PROTEIN  Length:205
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:205
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
          PAPS1_HUMAN    23 QRATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVP 227
               SCOP domains d2ofxa_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 2ofxA00 A:23-227 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhh........eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhh..hhhhhhhh....................eeee....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:23-59 UniProt: 21-59------------------------------------------------------------------------------Exon 1.5c  PDB: A:138-184 UniProt: 138-184     ---------------------------------------1.7b 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)
                 2ofx A  23 HMATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVP 227
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:205
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
          PAPS1_HUMAN    23 QRATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVP 227
               SCOP domains d2ofxb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 2ofxB00 B:23-227 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
           Pfam domains (1) ----------------------------APS_kinase-2ofxB01 B:51-209                                                                                                                                    ---------------PUA Pfam domains (1)
           Pfam domains (2) ----------------------------APS_kinase-2ofxB02 B:51-209                                                                                                                                    ---------------PUA Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhh.......eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh..hhhhhhhhh...................eee.....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:23-59 UniProt: 21-59------------------------------------------------------------------------------Exon 1.5c  PDB: B:138-184 UniProt: 138-184     ---------------------------------------1.7b Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.4c  PDB: B:59-137 UniProt: 59-137                                       ----------------------------------------------Exon 1.6  PDB: B:184-223                ---- Transcript 1 (2)
                 2ofx B  23 HMATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVP 227
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

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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/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: automated matches (303)

Protein domain: automated matches (303)

Human (Homo sapiens) [TaxId: 9606] (86)

1a	d2ofxa_	A:
1b	d2ofxb_	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)

1a	2ofxA00	A:23-227
1b	2ofxB00	B:23-227

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: APS_kinase (10)

Homo sapiens (Human) (7)

1a	APS_kinase-2ofxB01	B:51-209
1b	APS_kinase-2ofxB02	B:51-209

Clan: PUA (42)

Family: PUA_2 (11)

Homo sapiens (Human) (6)

2a	PUA_2-2ofxB03	B:225-227
2b	PUA_2-2ofxB04	B:225-227

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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	PAPS1_HUMAN \| O43252	:	1x6v 1xjq 1xnj 2ofw 2pey 2pez 2qjf

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