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Title :   THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

Authors :   M. J. Pugmire, S. E. Ealick

Date :   25 Aug 98 (Deposition) - 13 Jan 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Nucleoside Phosphorylase, Domain Movement, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Pugmire, S. E. Ealick
The Crystal Structure Of Pyrimidine Nucleoside Phosphorylase In A Closed Conformation.
Structure V. 6 1467 1998
PubMed-ID: 9817849 | Reference-DOI: 10.1016/S0969-2126(98)00145-2
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)
	Chains	:	A, B
	EC Number	:	2.4.2.2
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	PYNP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	URA	1	Ligand/Ion	URACIL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	AUTHOR	LYS A:187 , ARG A:168 , TYR A:165 , SER A:183 , SER A:182 , SER A:110 , LYS A:108 , THR A:120 , LYS A:81 , SER A:83	ACTIVE SITE
2	AC2	AUTHOR	LYS B:1187 , ARG B:1168 , TYR B:1165 , SER B:1183 , SER B:1182 , SER B:1110 , LYS B:1108 , THR B:1120 , LYS B:1081 , SER B:1083	ACTIVE SITE
3	AC3	SOFTWARE	LYS A:81 , HIS A:82 , SER A:83 , THR A:92 , LYS A:108 , SER A:110 , THR A:120 , HOH A:4003 , HOH A:4012 , HOH A:4105	BINDING SITE FOR RESIDUE PO4 A 2001
4	AC4	SOFTWARE	LYS B:1081 , HIS B:1082 , SER B:1083 , THR B:1092 , LYS B:1108 , SER B:1110 , THR B:1120 , HOH B:4066	BINDING SITE FOR RESIDUE PO4 B 2002
5	AC5	SOFTWARE	GLY A:88 , THR A:90 , LEU A:243 , ALA A:246 , GLU A:255	BINDING SITE FOR RESIDUE CA A 3001
6	AC6	SOFTWARE	GLY B:1088 , THR B:1090 , LEU B:1243 , ALA B:1246 , GLU B:1255	BINDING SITE FOR RESIDUE CA B 3002
7	AC7	SOFTWARE	HIS B:1082 , SER B:1083 , THR B:1084 , LEU B:1114 , TYR B:1165 , ARG B:1168 , ILE B:1180 , SER B:1183 , ILE B:1184 , LYS B:1187	BINDING SITE FOR RESIDUE URA B 5001
8	AC8	SOFTWARE	LYS B:1018 , GLU B:1022 , ARG B:1026 , GLN B:1064 , HOH B:4019	BINDING SITE FOR RESIDUE MES B 6001
9	AC9	SOFTWARE	TYR A:46 , ARG A:48 , GLY A:49 , ARG A:216 , HOH A:4021 , HOH A:4071	BINDING SITE FOR RESIDUE MES A 6002

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	PDP_GEOSE	110-125	2	A:110-125 B:1110-1125

(no "Exon" information available for 1BRW)

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:433
 aligned with PDP_GEOSE | P77836 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430   
           PDP_GEOSE      1 MRMVDLIEKKRDGHALTKEEIQFIIEGYTKGDIPDYQMSALAMAIFFRGMNEEETAELTMAMVHSGDTIDLSRIEGIKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDKLESVPGFHVEITNDEFIDLVNKNKIAVVGQSGNLTPADKKLYALRDVTATVNSIPLIASSIMSKKIAAGADAIVLDVKTGVGAFMKDLNDAKALAKAMVDIGNRVGRKTMAIISDMSQPLGYAIGNALEVKEAIDTLKGEGPEDFQELCLVLGSHMVYLAEKASSLEEARHMLEKAMKDGSALQTFKTFLAAQGGDASVVDDPSKLPQAKYIIELEAKEDGYVSEIVADAVGTAAMWLGAGRATKESTIDLAVGLVLRKKVGDAVKKGESLVTIYSNREQVDDVKQKLYENIRISATPVQAPTLIYDKIS  433
               SCOP domains d1brwa1 A:1-70 Pyrimidine nucleoside phosphorylase                    d1brwa2 A:71-330 Pyrimidine nucleoside phosphorylase                                                                                                                                                                                                                d1brwa3 A:331-433 Pyrimidine nucleoside phosphorylase                                                   SCOP domains
               CATH domains 1brwA03 A:1-67                                                     1brwA02 A:68-330,A:425-433 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                      1brwA01 A:331-424  [code=3.90.1170.30, no name defined]                                       1brwA02   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhh..............eeeee.......hhhhhhhhhhhh...eeeee.........hhhhhhh.........hhhhhhhhhhh.eeeee......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeeee...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhh...hhh.....eeeeee.....eeeee.hhhhhhhhhhh...............eeee............eeeeeee.....hhhhhhhh..eeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1brw A    1 MRMVDLIAKKRDGKALTKEEIEWIVRGYTNGDIPDYQMSALAMAIYFRGMTEEETAALTMAMVQSGEMLDLSSIRGVKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDKLESVPGFHVEISKDEFIRLVNENGIAIIGQTGDLTPADKKLYALRDVTATVNSIPLIASSIMSKKIAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVGRRTMAVISDMSQPLGYAVGNALEVKEAIETLKGNGPHDLTELCLTLGSHMVYLAEKAPSLDEARRLLEEAIRSGAAIAAFKTFLAAQGGDASVVDDLDKLPKAAYTSTVTAAADGYVAEMAADDIGTAAMWLGAGRAKKEDVIDLAVGIVLHKKIGDRVQKGEALATIHSNRPDVLDVKEKIEAAIRLSPQPVARPPLIYETIV  433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430

Chain B from PDB  Type:PROTEIN  Length:433
 aligned with PDP_GEOSE | P77836 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430   
           PDP_GEOSE      1 MRMVDLIEKKRDGHALTKEEIQFIIEGYTKGDIPDYQMSALAMAIFFRGMNEEETAELTMAMVHSGDTIDLSRIEGIKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDKLESVPGFHVEITNDEFIDLVNKNKIAVVGQSGNLTPADKKLYALRDVTATVNSIPLIASSIMSKKIAAGADAIVLDVKTGVGAFMKDLNDAKALAKAMVDIGNRVGRKTMAIISDMSQPLGYAIGNALEVKEAIDTLKGEGPEDFQELCLVLGSHMVYLAEKASSLEEARHMLEKAMKDGSALQTFKTFLAAQGGDASVVDDPSKLPQAKYIIELEAKEDGYVSEIVADAVGTAAMWLGAGRATKESTIDLAVGLVLRKKVGDAVKKGESLVTIYSNREQVDDVKQKLYENIRISATPVQAPTLIYDKIS  433
               SCOP domains d1brwb1 B:1001-1070 Pyrimidine nucleoside phosphorylase               d1brwb2 B:1071-1330 Pyrimidine nucleoside phosphorylase                                                                                                                                                                                                             d1brwb3 B:1331-1433 Pyrimidine nucleoside phosphorylase                                                 SCOP domains
               CATH domains 1brwB03 B:1001-1067                                                1brwB02 B:1068-1330,B:1425-1433 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                 1brwB01 B:1331-1424  [code=3.90.1170.30, no name defined]                                     1brwB02   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhh...eeeee.........hhhhhhh.........hhhhhhhhhh..eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeeee.......eee.hhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhh..hhh.....eeeeee...........hhhhhhhhhh................eeee............eeeeeee.....hhhhhhhhhh.............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1brw B 1001 MRMVDLIAKKRDGKALTKEEIEWIVRGYTNGDIPDYQMSALAMAIYFRGMTEEETAALTMAMVQSGEMLDLSSIRGVKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDKLESVPGFHVEISKDEFIRLVNENGIAIIGQTGDLTPADKKLYALRDVTATVNSIPLIASSIMSKKIAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVGRRTMAVISDMSQPLGYAVGNALEVKEAIETLKGNGPHDLTELCLTLGSHMVYLAEKAPSLDEARRLLEEAIRSGAAIAAFKTFLAAQGGDASVVDDLDKLPKAAYTSTVTAAADGYVAEMAADDIGTAAMWLGAGRAKKEDVIDLAVGIVLHKKIGDRVQKGEALATIHSNRPDVLDVKEKIEAAIRLSPQPVARPPLIYETIV 1433
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430

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 '\|'

(no "Pfam Domain" information available for 1BRW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDP_GEOSE | P77836)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004645	phosphorylase activity	Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
	GO:0016154	pyrimidine-nucleoside phosphorylase activity	Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	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:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0006213	pyrimidine nucleoside metabolic process	The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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