3G3R - JenaLib

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Title :   CRYSTAL STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH APPNHP-MN2+

Authors :   M. Hothorn

Date :   02 Feb 09 (Deposition) - 05 May 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Polyphosphate Polymerase, Polyphosphate Kinase, Vtc Complex, Vacuolar Transporter Chaperone, Tunnel Enzyme, Membrane, Phosphoprotein, Transmembrane, Vacuole, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hothorn, H. Neumann, E. D. Lenherr, M. Wehner, V. Rybin, P. O. Hassa, A. Uttenweiler, M. Reinhardt, A. Schmidt, J. Seiler, A. G. Ladurner, C. Herrmann, K. Scheffzek, A. Mayer
Catalytic Core Of A Membrane-Associated Eukaryotic Polyphosphate Polymerase.
Science V. 324 513 2009
PubMed-ID: 19390046 | Reference-DOI: 10.1126/SCIENCE.1168120
(for further references see the PDB file header)

Molecule 1 - VACUOLAR TRANSPORTER CHAPERONE 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21 (DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 189-480
	Gene	:	J1345, PHM3, VTC4, YJL012C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PHOSPHATE METABOLISM PROTEIN 3

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	NA	1	Ligand/Ion	SODIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:12 , HOH A:42 , LYS A:200 , ARG A:264 , ARG A:266 , LYS A:281 , LYS A:294 , TYR A:359 , ARG A:361 , GLU A:426 , SER A:457 , LYS A:458 , HOH A:537 , MN A:1001	BINDING SITE FOR RESIDUE ANP A 1000
02	AC2	SOFTWARE	GLU A:426 , HOH A:494 , ANP A:1000	BINDING SITE FOR RESIDUE MN A 1001
03	AC3	SOFTWARE	SER A:272 , THR A:273 , ASP A:274 , THR A:275 , HOH A:486 , HOH A:536	BINDING SITE FOR RESIDUE SO4 A 2
04	AC4	SOFTWARE	HOH A:154 , HOH A:158 , LYS A:300 , ARG A:302 , HIS A:303 , LYS A:320	BINDING SITE FOR RESIDUE SO4 A 5
05	AC5	SOFTWARE	LYS A:396 , HOH A:512 , HOH B:26 , ASN B:246	BINDING SITE FOR RESIDUE SO4 A 7
06	AC6	SOFTWARE	ASP A:274 , GLU A:301 , ARG A:302	BINDING SITE FOR RESIDUE NA A 1
07	AC7	SOFTWARE	HOH B:1 , HOH B:127 , HOH B:137 , LYS B:200 , TYR B:241 , ARG B:264 , ARG B:266 , LYS B:281 , LYS B:294 , TYR B:359 , ARG B:361 , GLU B:426 , PHE B:456 , SER B:457 , LYS B:458 , MN B:1001	BINDING SITE FOR RESIDUE ANP B 1000
08	AC8	SOFTWARE	HOH B:174 , GLU B:426 , ANP B:1000	BINDING SITE FOR RESIDUE MN B 1001
09	AC9	SOFTWARE	LYS A:470 , HOH A:493 , ARG B:302 , HIS B:303 , LYS B:320	BINDING SITE FOR RESIDUE SO4 B 3
10	BC1	SOFTWARE	HOH B:39 , HOH B:104 , ARG B:253 , LYS B:256 , HIS B:283 , SER B:292 , HOH B:491 , HOH B:533	BINDING SITE FOR RESIDUE SO4 B 4
11	BC2	SOFTWARE	THR B:273 , ASP B:274 , THR B:275 , HOH B:496	BINDING SITE FOR RESIDUE SO4 B 6

(no "SS Bond" information available for 3G3R)

Asymmetric Unit

No.	Residues
1	Trp A:407	-	Pro A:408
2	Leu A:433	-	Gly A:434
3	Trp B:407	-	Pro B:408
4	Leu B:433	-	Gly B:434

(no "SAP(SNP)/Variant" information available for 3G3R)

(no "PROSITE Motif" information available for 3G3R)

(no "Exon" information available for 3G3R)

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:286
 aligned with VTC4_YEAST | P47075 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:286
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
           VTC4_YEAST   195 VRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQ 480
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhh...eee.......hhhh.eeeeeeee...hhhhhhhhhh....eeeeeeee......eeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee............................hhh.eee...eeeeeeee.......hhhhhhhhhh...ee....hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g3r A 195 VRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQ 480
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with VTC4_YEAST | P47075 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:287
                                   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       
           VTC4_YEAST   193 NFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLP 479
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhhhh.....eee...--......eeeeeeee...hhhhhhhhhh....eeeeeeee......eeeeeeee..hhhhh...eeeeeeee..hhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee............................hhh.eee...eeeeeeeeee.....hhhhhhhhh....ee....hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g3r B 193 NFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTN--FEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLP 479
                                   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       
                                                            227  |                                                                                                                                                                                                                                                         
                                                               230

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 "SCOP Domain" information available for 3G3R)

(no "CATH Domain" information available for 3G3R)

(no "Pfam Domain" information available for 3G3R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (VTC4_YEAST | P47075)

molecular function
	GO:0008976	polyphosphate kinase activity	Catalysis of the reaction: ATP + phosphate(n) = ADP + phosphate(n+1).
	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).
biological process
	GO:0016237	lysosomal microautophagy	The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
	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:0006797	polyphosphate metabolic process	The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.
	GO:0007034	vacuolar transport	The directed movement of substances into, out of or within a vacuole.
	GO:0042144	vacuole fusion, non-autophagic	The fusion of two vacuole membranes to form a single vacuole.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0000329	fungal-type vacuole membrane	The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031310	intrinsic component of vacuolar membrane	The component of the vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
	GO:0033254	vacuolar transporter chaperone complex	A protein complex that contains four related proteins that have been implicated in several membrane-related processes, such as sorting of H+-translocating ATPases, endocytosis, ER-Golgi trafficking, vacuole fusion, vacuolar polyphosphate homeostasis and the microautophagic scission of vesicles into the vacuolar lumen. The complex is enriched at the vacuolar membrane, but also found in other cellular compartments, including the ER and the cell periphery. In Saccharomyces, the subunits are Vtc1p, Vtc2p, Vtc3p and Vtc4p.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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	Cis Peptide Bonds
		Leu A:433 - Gly A:434	[ RasMol ]
		Leu B:433 - Gly B:434	[ RasMol ]
		Trp A:407 - Pro A:408	[ RasMol ]
		Trp B:407 - Pro B:408	[ RasMol ]

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	3g3r
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	VTC4_YEAST \| P47075	:	3g3q 3g3t 3g3u 5iig 5iiq 5iit 5lnc

3g3o	CRYSTAL STRUCTURE OF THE CATALYTICALLY IMPAIRED SUBUNIT VTC2P THAT IS PART OF THE SAME MEMBRANE-INTEGRAL PROTEIN COMPLEX
3g3q	EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH A PHOSPHATE POLYMER
3g3t	STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH ORTHOPHOSPHATE
3g3u	STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH PYROPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (15, 15)

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