1VBG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PYRUVATE PHOSPHATE DIKINASE FROM MAIZE

Authors :   T. Nakanishi, T. Nakatsu, M. Matsuoka, K. Sakata, H. Kato, Riken Struc Genomics/Proteomics Initiative (Rsgi)

Date :   26 Feb 04 (Deposition) - 08 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transferase, Maize, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakanishi, T. Nakatsu, M. Matsuoka, K. Sakata, H. Kato
Crystal Structures Of Pyruvate Phosphate Dikinase From Maiz Revealed An Alternative Conformation In The Swiveling-Domai Motion
Biochemistry V. 44 1136 2005
PubMed-ID: 15667207 | Reference-DOI: 10.1021/BI0484522
(for further references see the PDB file header)

Molecule 1 - PYRUVATE,ORTHOPHOSPHATE DIKINASE
	Chains	:	A
	EC Number	:	2.7.9.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-2
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577
	Synonym	:	PYRUVATE PHOSPHATE DIKINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:750 , ASP A:774 , HOH A:3003 , HOH A:3008 , HOH A:3017 , HOH A:3020	BINDING SITE FOR RESIDUE MG A 2000
2	AC2	SOFTWARE	ARG A:564 , ARG A:621 , HOH A:3008 , HOH A:3017 , HOH A:3024 , HOH A:3175 , HOH A:3179 , HOH A:3184 , HOH A:3232 , HOH A:3243	BINDING SITE FOR RESIDUE SO4 A 3000
3	AC3	SOFTWARE	ASN A:542 , ARG A:564 , GLY A:837 , GLU A:838 , SER A:860 , HOH A:3055 , HOH A:3185 , HOH A:3232	BINDING SITE FOR RESIDUE SO4 A 3001
4	AC4	SOFTWARE	ALA A:519 , LEU A:520 , SER A:521	BINDING SITE FOR RESIDUE SO4 A 3002

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

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

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEP_ENZYMES_PHOS_SITE	PS00370	PEP-utilizing enzymes phosphorylation site signature.	PPDK1_MAIZE	524-535	1	A:453-464
2	PEP_ENZYMES_2	PS00742	PEP-utilizing enzymes signature 2.	PPDK1_MAIZE	837-855	1	A:766-784

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEP_ENZYMES_PHOS_SITE	PS00370	PEP-utilizing enzymes phosphorylation site signature.	PPDK1_MAIZE	524-535	2	A:453-464
2	PEP_ENZYMES_2	PS00742	PEP-utilizing enzymes signature 2.	PPDK1_MAIZE	837-855	2	A:766-784

(no "Exon" information available for 1VBG)

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:874
 aligned with PPDK1_MAIZE | P11155 from UniProtKB/Swiss-Prot  Length:947

    Alignment length:874
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943    
          PPDK1_MAIZE    74 KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAAGLAAKSGERFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSAKGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAVNVQCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEGLVEPRSAIKMVEPGHLDQLLHPQFENPSAYKDQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTERGGMTSHAAVVARWWGKCCVSGCSGIRVNDAEKLVTIGSHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLLTYQRSDFEGIFRAMDGLPVTIRLLDHPSYEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQGVQVFPEIMVPLVGTPQELGHQVTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVHLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGEHGGEPSSVAFFAKAGLDFVSCSPFRVPIARLAAAQVLV 947
               SCOP domains d1vbga3 A:3-382 Pyruvate phosphate dikinase, N-terminal domain                                                                                                                                                                                                                                                                                                                              d1vbga2 A:383-517 Pyruvate phosphate dikinase, central domain                                                                          ---d1vbga1 A:521-876 Pyruvate phosphate dikinase, C-terminal domain                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vbgA01 A:3-114,A:200-246 ATP-grasp fold, A domain                                                              1vbgA02 A:115-199  [code=1.20.80.30, no name defined]                                1vbgA01 A:3-114,A:200-246                      1vbgA03 A:247-344 ATP-grasp fold, B domain                                                        1vbgA04 A:345-385,A:513-534              1vbgA05 A:386-510 Phosphohistidine domains of PEP-utilising enzymes                                                          --1vbgA04               1vbgA06 A:535-876 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------PPDK_N-1vbgA03 A:16-365                                                                                                                                                                                                                                                                                                                                       --------------------------------------------------PEP-utilizers-1vbgA02 A:416-506                                                            -----------PEP-utilizers_C-1vbgA01 A:518-876                                                                                                                                                                                                                                                                                                                                       Pfam domains
         Sec.struct. author ...eeeee..ee.........hhhhhhhhhhhhhh......eeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...........eeee.............eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhh..........eeeee..........eeeeee...........eeeeee..hhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhh..eeee.eeee..eeeeeee.hhhhhhhhhhh...eeeee......hhhhhhhh.eeee......hhhhhhhhhh...eee....eeee....eeee..eeee...eeeee....eeee...........hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeeehhhhhhhhhhh....hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_2      -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbg A   3 KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAAGLAAKSGERFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSAKGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAVNVQCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEGLVEPRSAIKMVEPGHLDQLLHPQFENPSAYKDQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTERGGMTSHAAVVARGWGKCCVSGCSGIRVNDAEKLVTIGGHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLLPYQRSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQGVQVFPEIMVPLVGTPQELGHQVTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVYLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGEHGGEPSSVAFFAKAGLDYVSCSPFRVPIARLAAAQVLV 876
                                    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       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872

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 Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: PEP-utilizers_C (11)

Zea mays (Maize) (2)

PEP-utilizers_C-1vbgA01

A:518-876

Clan: no clan defined [family: PEP-utilizers] (11)

Family: PEP-utilizers (11)

Zea mays (Maize) (2)

PEP-utilizers-1vbgA02

A:416-506

Clan: no clan defined [family: PPDK_N] (7)

Family: PPDK_N (7)

Zea mays (Maize) (2)

PPDK_N-1vbgA03

A:16-365

Asymmetric Unit(hide GO term definitions)

Chain A (PPDK1_MAIZE | P11155)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0050242	pyruvate, phosphate dikinase activity	Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H(+) + phosphoenolpyruvate.
	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:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
	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:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vbg)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1vbg
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PPDK1_MAIZE \| P11155
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.9.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PPDK1_MAIZE \| P11155
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PPDK1_MAIZE \| P11155	:	1vbh

1vbh	PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PEP RELATED ID: MY_001000036.1 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (6, 6)

Pfam Domains (3, 3)

Gene Ontology (14, 14)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File