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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE EXOCYTOSIS-SENSITIVE PHOSPHOPROTEIN, PP63/PARAFUSIN (PHOSPHOGLUCOMUTASE) FROM PARAMECIUM

Authors :   S. Mueller, K. Diederichs, J. Breed, R. Kissmehl, K. Hauser, H. Plattner, W. Welte

Date :   21 Nov 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Parafusin, Phosphoprotein Pp63, Exocytosis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Muller, K. Diederichs, J. Breed, R. Kissmehl, K. Hauser, H. Plattner, W. Welte
Crystal Structure Analysis Of The Exocytosis-Sensitive Phosphoprotein, Pp63/Parafusin (Phosphoglucomutase), From Paramecium Reveals Significant Conformational Variability.
J. Mol. Biol. V. 315 141 2002
PubMed-ID: 11779235 | Reference-DOI: 10.1006/JMBI.2001.5168
(for further references see the PDB file header)

Molecule 1 - PHOSPHOGLUCOMUTASE 1
	Chains	:	A, B
	EC Number	:	5.4.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PARAMECIUM TETRAURELIA
	Organism Taxid	:	5888

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:308 , ASP A:310 , ASP A:312 , SO4 A:601	BINDING SITE FOR RESIDUE ZN A 700
2	AC2	SOFTWARE	SER A:126 , HIS A:127 , ASP A:308 , ASP A:310 , ASP A:312 , ARG A:313 , LYS A:405 , ZN A:700	BINDING SITE FOR RESIDUE SO4 A 601
3	AC3	SOFTWARE	THR A:23 , ARG A:515 , SER A:517 , GLY A:518 , THR A:519 , ARG A:527	BINDING SITE FOR RESIDUE SO4 A 603
4	AC4	SOFTWARE	ASP B:308 , ASP B:310 , ASP B:312 , SO4 B:602	BINDING SITE FOR RESIDUE ZN B 700
5	AC5	SOFTWARE	SER B:126 , HIS B:127 , ASP B:308 , ASP B:312 , ARG B:313 , TRP B:375 , ZN B:700	BINDING SITE FOR RESIDUE SO4 B 602
6	AC6	SOFTWARE	ARG B:515 , SER B:517 , GLY B:518 , THR B:519 , ARG B:527	BINDING SITE FOR RESIDUE SO4 B 604

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	PGM1_PARTE	120-129	2	A:120-129 B:120-129

(no "Exon" information available for 1KFI)

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:570
 aligned with PGM1_PARTE | P47244 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:570
                                    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       492       502       512       522       532       542       552       562       572
           PGM1_PARTE     3 QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGIILTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVAGPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAAKNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNKADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT 572
               SCOP domains d1kfia1 A:3-205 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                                                                                                        d1kfia2 A:206-323 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                 d1kfia3 A:324-443 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                   d1kfia4 A:444-572 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                             SCOP domains
               CATH domains 1kfiA01 A:3-212 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                                                                                                             1kfiA02 A:213-321 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                      1kfiA03 A:322-447 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                       1kfiA04 A:448-572 Major birch pollen allergen Bet v 1                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.............eeeehhhhh..hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhhhhhh..eeeeeee............eeeeeee.......hhhhhhhhhhhhh...eeee...hhhhh......eeeeee.......eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhh.ee......hhhhh........hhhhhhhh......hhhhh..eeeee......eeeee..eeehhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh..eeee..hhhhhhhhhhh....eeee...eeee......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh.....eeee..ee......ee....eeee.....eeeeee.......eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PGM_PMM   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kfi A   3 QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGIILTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVAGPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAAKNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNKADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT 572
                                    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       492       502       512       522       532       542       552       562       572

Chain B from PDB  Type:PROTEIN  Length:570
 aligned with PGM1_PARTE | P47244 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:570
                                    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       492       502       512       522       532       542       552       562       572
           PGM1_PARTE     3 QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGIILTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVAGPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAAKNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNKADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT 572
               SCOP domains d1kfib1 B:3-205 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                                                                                                        d1kfib2 B:206-323 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                 d1kfib3 B:324-443 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                   d1kfib4 B:444-572 Exocytosis-sensitive phosphoprotein, pp63/parafusin                                                             SCOP domains
               CATH domains 1kfiB01 B:3-212 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                                                                                                             1kfiB02 B:213-321 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                      1kfiB03 B:322-447 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                       1kfiB04 B:448-572 Major birch pollen allergen Bet v 1                                                                         CATH domains
           Pfam domains (1) ---------------PGM_PMM_I-1kfiB07 B:18-168                                                                                                                             --------------------------------------PGM_PMM_II-1kfiB03 B:207-320                                                                                      ----PGM_PMM_III-1kfiB01 B:325-442                                                                                         ------------PGM_PMM_IV-1kfiB05 B:455-551                                                                     --------------------- Pfam domains (1)
           Pfam domains (2) ---------------PGM_PMM_I-1kfiB08 B:18-168                                                                                                                             --------------------------------------PGM_PMM_II-1kfiB04 B:207-320                                                                                      ----PGM_PMM_III-1kfiB02 B:325-442                                                                                         ------------PGM_PMM_IV-1kfiB06 B:455-551                                                                     --------------------- Pfam domains (2)
         Sec.struct. author ......eeee.............eeeehhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhhhhhh..eeeeeee............eeeeeee.......hhhhhhhhhhhhhh..eeee...hhhhhh.....eeeeee.......eeeeeee..hhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh.....hhh.ee......hhhhh........hhhhhhhh......hhhhh..eeee........eeee..eeehhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh..eeee...hhhhhhhhhh....eeee...eee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...eeee..ee......ee....eeee.....eeeeee.......eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PGM_PMM   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kfi B   3 QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGIILTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVAGPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAAKNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNKADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT 572
                                    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       492       502       512       522       532       542       552       562       572

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: Major birch pollen allergen Bet v 1 (22)

Paramecium tetraurelia. Organism_taxid: 5888. (2)

1a	1kfiA04	A:448-572
1b	1kfiB04	B:448-572

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

Topology: Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 (24)

Homologous Superfamily: Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 (24)

Paramecium tetraurelia. Organism_taxid: 5888. (2)

2a	1kfiA03	A:322-447
2b	1kfiB03	B:322-447
2c	1kfiA01	A:3-212
2d	1kfiB01	B:3-212
2e	1kfiA02	A:213-321
2f	1kfiB02	B:213-321

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PGM1_PARTE | P47244)

molecular function
	GO:0016868	intramolecular transferase activity, phosphotransferases	Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0004614	phosphoglucomutase activity	Catalysis of the reaction: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0071704	organic substance metabolic process	The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1kfi)

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	PGM1_PARTE \| P47244	:	1kfq

1kfq	1KFQ IS THE SAME PROTEIN IN THE OPEN FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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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SCOP Domains (2, 8)

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