2VGG	Transferase	date	Nov 13, 2007
title	Human Erythrocyte Pyruvate Kinase: R479h Mutant
authors	G.Valentini, L.R.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Ab C.Wang, P.Bianchi, A.Zanella, A.Mattevi
compound		source
Molecule: Pyruvate Kinase Isozymes Rl Chain: A, B, C, D Fragment: Residues 47-574 Synonym: R-Typel-Type Pyruvate Kinase, Red Cellliver Pyru Kinase, Pyruvate Kinase 1pyruvate Kinase; Ec: 2.7.1.40 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21
symmetry	Space Group: P 1 21 1	R_factor 0.253 R_Free 0.294
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.036 171.795 85.086 90.00 91.17 90.00
method	X-Ray Diffraction	resolution	2.74 Å
ligand	FBP, K, MN, PGA	enzyme	Transferase E.C.2.7.1.40 BRENDA
note	2VGG supersedes 1LIY
Gene Ontology	Chain Function Process Component A, D, C, B nucleotide binding catalytic activity pyruvate kinase activity ATP binding kinase activity transferase activity metal ion binding response to hypoxia carbohydrate metabolic proce... glucose metabolic process glycolysis energy reserve metabolic pro... ATP biosynthetic process response to nutrient metabolic process response to heat response to glucose stimulus... response to metal ion response to lithium ion response to organic cyclic c... phosphorylation endocrine pancreas developme... positive regulation of cellu... cellular response to insulin... response to ATP pyruvate biosynthetic proces... small molecule metabolic pro... response to cAMP response to other organism cytosol
Primary reference	Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia., Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A, J Biol Chem. 2002 Jun 28;277(26):23807-14. Epub 2002 Apr 17. PMID:11960989

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (317 Kb) [Save to disk] Biological Unit Coordinates (2vgg.pdb1.gz) 305 Kb LPC: Ligand-Protein Contacts for 2VGG CSU: Contacts of Structural Units for 2VGG Likely Quarternary Molecular Structure file(s) for 2VGG Structure Factors (452 Kb) Retrieve 2VGG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VGG from S2C, [Save to disk] Re-refined 2vgg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VGG in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2VGG

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2VGG, from MSDmotif at EBI Fold representative 2vgg from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vgg_A] [2vgg_B] [2vgg_C] [2vgg_D] SWISS-PROT database: [P30613] Domain organization of [KPYR_HUMAN] by SWISSPFAM Alignments of the sequence of 2VGG with the sequences similar proteins can be viewed for 2VGG's classification [KPYR_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [KPYR_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2VGG

Community annotation for 2VGG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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