2NMP	Lyase	date	Oct 23, 2006
title	Crystal Structure Of Human Cystathionine Gamma Lyase
authors	T.Karlberg, J.Uppenberg, C.Arrowsmith, H.Berglund, R.D.Busam, R.C A.Edwards, U.B.Ericsson, S.Flodin, A.Flores, S.Graslund, B.M.Hal M.Hammarstrom, M.Hogbom, I.Johansson, T.Kotenyova, A.Magnusdott M.Moche, M.E.Nilsson, P.Nordlund, T.Nyman, D.Ogg, C.Persson, J.Sa P.Stenmark, M.Sundstrom, A.G.Thorsell, S.Van-Den-Berg, K.Wallde J.Weigelt, L.Holmberg-Schiavone, Structural Genomics Consorti
compound		source
Molecule: Cystathionine Gamma-Lyase Chain: A, B, C, D Fragment: Residues 1-402 Synonym: Gamma-Cystathionase Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cth Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl-21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pnic-Bsa4
symmetry	Space Group: P 21 21 21	R_factor 0.177 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 105.780 107.570 153.310 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	PLP	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B cystathionine gamma-lyase ac... protein binding calmodulin binding lyase activity carbon-sulfur lyase activity... pyridoxal phosphate binding L-cystine L-cysteine-lyase (... homocysteine desulfhydrase a... L-cysteine desulfhydrase act... sulfur amino acid metabolic ... sulfur amino acid catabolic ... cysteine metabolic process cellular amino acid biosynth... protein-pyridoxal-5-phosphat... cysteine biosynthetic proces... transsulfuration endoplasmic reticulum unfold... cellular nitrogen compound m... negative regulation of apopt... positive regulation of I-kap... small molecule metabolic pro... protein sulfhydration positive regulation of NF-ka... protein homotetramerization hydrogen sulfide biosyntheti... nucleus cytoplasm cytosol
Primary reference	Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S., Sun Q, Collins R, Huang S, Holmberg-Schiavone L, Anand GS, Tan CH, van-den-Berg S, Deng LW, Moore PK, Karlberg T, Sivaraman J, J Biol Chem. 2009 Jan 30;284(5):3076-85. Epub 2008 Nov 19. PMID:19019829

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk] Biological Unit Coordinates (2nmp.pdb1.gz) 240 Kb LPC: Ligand-Protein Contacts for 2NMP CSU: Contacts of Structural Units for 2NMP Likely Quarternary Molecular Structure file(s) for 2NMP Structure Factors (450 Kb) Retrieve 2NMP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2NMP from S2C, [Save to disk] Re-refined 2nmp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2NMP 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 2NMP

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 2NMP, from MSDmotif at EBI Fold representative 2nmp from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2nmp_A] [2nmp_B] [2nmp_C] [2nmp_D] SWISS-PROT database: [P32929] Domain organization of [CGL_HUMAN] by SWISSPFAM Alignments of the sequence of 2NMP with the sequences similar proteins can be viewed for 2NMP's classification [CGL_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 [CGL_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2NMP

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

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---