2JBH - JenaLib

Title :   HUMAN PHOSPHORIBOSYL TRANSFERASE DOMAIN CONTAINING 1

Authors :   M. Welin, P. Stenmark, C. Arrowsmith, H. Berglund, R. Busam, R. Collins A. Edwards, H. Eklund, U. B. Ericsson, S. Flodin, A. Flores, S. Graslun M. Hammarstrom, B. M. Hallberg, L. Holmberg Schiavone, M. Hogbom, I. Johansson, T. Karlberg, T. Kotenyova, M. Moche, M. E. Nilsson, T. Ny D. Ogg, C. Persson, J. Sagemark, M. Sundstrom, J. Uppenberg, A. G. Thor S. Van Den Berg, J. Weigelt, P. Nordlund

Date :   07 Dec 06 (Deposition) - 20 Dec 06 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Glycosyltransferase, Transferase, Purine Salvage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, L. Egeblad, A. Johansson, P. Stenmark, L. Wang, S. Flodin, T. Nyman, L. Tresaugues, T. Kotenyova, I. Johansson, S. Eriksson, H. Eklund, P. Nordlund
Structural And Functional Studies Of The Human Phosphoribosyltransferase Domain Containing Protein 1.
Febs J. V. 277 4920 2010
PubMed-ID: 21054786 | Reference-DOI: 10.1111/J.1742-4658.2010.07897.X

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:75 , LYS A:76 , GLY A:77 , ASP A:201 , ARG A:207 , CA A:1229 , HOH A:2139 , HOH A:2140 , HOH A:2141 , HOH A:2142 , HOH A:2145	BINDING SITE FOR RESIDUE PO4 A1227
2	AC2	SOFTWARE	GLU A:141 , ASP A:142 , 5GP A:1230 , HOH A:2140 , HOH A:2141 , HOH A:2143	BINDING SITE FOR RESIDUE CA A1228
3	AC3	SOFTWARE	ASP A:201 , PO4 A:1227 , HOH A:2118 , HOH A:2127 , HOH A:2145 , HOH B:2089 , HOH B:2090	BINDING SITE FOR RESIDUE CA A1229
4	AC4	SOFTWARE	LEU B:75 , LYS B:76 , GLY B:77 , ASP B:201 , ARG B:207 , CA B:1228 , HOH B:2075 , HOH B:2108 , HOH B:2141 , HOH B:2142 , HOH B:2144 , HOH B:2145	BINDING SITE FOR RESIDUE PO4 B1227
5	AC5	SOFTWARE	ASP B:201 , PO4 B:1227 , HOH B:2127 , HOH B:2128 , HOH B:2143 , HOH B:2147	BINDING SITE FOR RESIDUE CA B1228
6	AC6	SOFTWARE	GLU B:141 , ASP B:142 , 5GP B:1230 , HOH B:2142 , HOH B:2144 , HOH B:2153	BINDING SITE FOR RESIDUE CA B1229
7	AC7	SOFTWARE	GLU A:141 , ASP A:142 , VAL A:143 , GLY A:145 , THR A:146 , GLY A:147 , ARG A:148 , THR A:149 , LYS A:173 , PHE A:194 , VAL A:195 , LEU A:200 , ASP A:201 , CA A:1228 , HOH A:2142 , HOH A:2143 , HOH A:2144 , HOH A:2145 , HOH A:2146 , HOH A:2147 , HOH A:2148 , GLN B:116 , HOH B:2087	BINDING SITE FOR RESIDUE 5GP A1230
8	AC8	SOFTWARE	GLU B:141 , ASP B:142 , VAL B:143 , GLY B:145 , THR B:146 , GLY B:147 , ARG B:148 , THR B:149 , LYS B:173 , LEU B:193 , PHE B:194 , VAL B:195 , ASP B:201 , CA B:1229 , HOH B:2108 , HOH B:2146 , HOH B:2147 , HOH B:2148 , HOH B:2150 , HOH B:2152 , HOH B:2153	BINDING SITE FOR RESIDUE 5GP B1230

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (9, 18)

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000320152	1a	ENSE00001124245	chr10:25241533-25241457	77	PRDC1_HUMAN	1-16	16	2	A:7-16 B:9-16	10 8
1.2	ENST00000320152	2	ENSE00001344078	chr10:25231365-25231259	107	PRDC1_HUMAN	17-52	36	2	A:17-52 B:17-52	36 36
1.3	ENST00000320152	3	ENSE00001344073	chr10:25226296-25226113	184	PRDC1_HUMAN	52-113	62	2	A:52-110 B:52-113	59 62
1.5	ENST00000320152	5	ENSE00001344069	chr10:25160992-25160927	66	PRDC1_HUMAN	114-135	22	2	A:121-135 B:114-135	15 22
1.6	ENST00000320152	6	ENSE00001702650	chr10:25147338-25147321	18	PRDC1_HUMAN	136-141	6	2	A:136-141 B:136-141	6 6
1.7b	ENST00000320152	7b	ENSE00001344065	chr10:25145924-25145842	83	PRDC1_HUMAN	142-169	28	2	A:142-169 B:142-169	28 28
1.8	ENST00000320152	8	ENSE00001344061	chr10:25144293-25144247	47	PRDC1_HUMAN	169-185	17	2	A:169-185 (gaps) B:169-185 (gaps)	17 17
1.9	ENST00000320152	9	ENSE00001344057	chr10:25140393-25140317	77	PRDC1_HUMAN	185-210	26	2	A:185-210 B:185-210	26 26
1.10b	ENST00000320152	10b	ENSE00001649958	chr10:25138820-25137554	1267	PRDC1_HUMAN	211-225	15	2	A:211-225 B:211-225	15 15

Sequences/Alignments

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:208
 aligned with PRDC1_HUMAN | Q9NRG1 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
          PRDC1_HUMAN     7 EAPDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDIMKDIGYSDIMVLCVLKGGYKFCADLVEHLKNISRNSDRFVSMKVDFIRLKSYRNDQSMGEMQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRTSRSDGFRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV 225
               SCOP domains d2jbha_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 2jbhA00 A:7-225  [code=3.40.50.2020, no name defined]                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.....eeeeeeee.----------..ee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee..-........eeeeee.....................eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a Exon 1.2  PDB: A:17-52              -------------------------------------------------------------Exon 1.5 [INCOMPLETE] 1.6   Exon 1.7b  PDB: A:142-169   ---------------Exon 1.9  PDB: A:185-210  Exon 1.10b      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:52-110 UniProt: 52-113 [INCOMPLETE]          -------------------------------------------------------Exon 1.8         ---------------------------------------- Transcript 1 (2)
                 2jbh A   7 EAPDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDIMKDIGYSDIMVLCVLKGGYKFcADLVEHLKNISRNSDRFVSMKVDFIRLK----------MQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRT-RSDGFRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV 225
                                    16        26        36        46        56        66        76     |  86        96       106   |     -    |  126       136       146       156       166        |-|      186       196       206       216         
                                                                                                      82-CAS                     110        121                                                   175 |                                                
                                                                                                                                                                                                    177

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with PRDC1_HUMAN | Q9NRG1 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:217
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       
          PRDC1_HUMAN     9 PDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDIMKDIGYSDIMVLCVLKGGYKFCADLVEHLKNISRNSDRFVSMKVDFIRLKSYRNDQSMGEMQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRTSRSDGFRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV 225
               SCOP domains d2jbhb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 2jbhB00 B:9-225  [code=3.40.50.2020, no name defined]                                                                                                                                                                     CATH domains
           Pfam domains (1) ---------------------------------Pribosyltran-2jbhB01 B:42-171                                                                                                     ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------Pribosyltran-2jbhB02 B:42-171                                                                                                     ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhh...eeeeeeeeeeeeee.....eeeeee...hhhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee..----.....eeeeee.....................eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a    Exon 1.2  PDB: B:17-52              -------------------------------------------------------------Exon 1.5              1.6   Exon 1.7b  PDB: B:142-169   ---------------Exon 1.9  PDB: B:185-210  Exon 1.10b      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:52-113 UniProt: 52-113                       -------------------------------------------------------Exon 1.8         ---------------------------------------- Transcript 1 (2)
                 2jbh B   9 PDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDIMKDIGYSDIMVLCVLKGGYKFcADLVEHLKNISRNSDRFVSMKVDFIRLKSYRNDQSMGEMQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRT----GFRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV 225
                                    18        28        38        48        58        68        78   |    88        98       108       118       128       138       148       158       168      |  - |     188       198       208       218       
                                                                                                    82-CAS                                                                                      175  180

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRDC1_HUMAN | Q9NRG1)

molecular function
	GO:0004422	hypoxanthine phosphoribosyltransferase activity	Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0046038	GMP catabolic process	The chemical reactions and pathways resulting in the breakdown of GMP, guanosine monophosphate.
	GO:0032263	GMP salvage	Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
	GO:0032264	IMP salvage	Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
	GO:0006168	adenine salvage	Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
	GO:0006178	guanine salvage	Any process that generates guanine, 2-amino-6-hydroxypurine, from derivatives of it without de novo synthesis.
	GO:0046100	hypoxanthine metabolic process	The chemical reactions and pathways involving hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0006166	purine ribonucleoside salvage	Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
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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