PDBsum entry: 1kmk

Lyase

PDB id: 1kmk

Contents

Protein chain

405 a.a. *

Ligands

CSE-PLP

Waters ×485

* Residue conservation analysis

PDB id:

1kmk

Name:

Lyase

Title:

E. Coli nifs/csdb protein at 2.20a with the cysteine persele intermediate (residue csz).

Structure:

Selenocysteine lyase. Chain: a. Synonym: nifs/csdb, selenocysteine reductase, selenocystein lyase, scl. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.196 R-free: 0.239

Authors:

C.D.Lima,S.K.Burley,New York Sgx Research Center For Structu Genomics (Nysgxrc)

Key ref:

V.Bernier-Villamor et al. (2002). Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. Cell, 108, 345-356. PubMed id: 11853669 DOI: 10.1016/S0092-8674(02)00630-X

Date:

16-Dec-01 Release date: 21-Dec-01

Protein chain

P77444  (SUFS_ECOLI) -  Cysteine desulfurase

Seq: 406 a.a.

Struc: 405 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.2.8.1.7 - Cysteine desulfurase.
• Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor

L-cysteine + acceptor = L-alanine (Bound ligand (Het Group name = CSE) matches with 71.43% similarity) + S-sulfanyl-acceptor

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

• Enzyme class 2: E.C.4.4.1.16 - Selenocysteine lyase.
• Reaction: L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor

L-selenocysteine + reduced acceptor = selenide + L-alanine (Bound ligand (Het Group name = CSE) matches with 71.43% similarity) + acceptor

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1016/S0092-8674(02)00630-X

Cell 108:345-356 (2002)

PubMed id: 11853669

Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1.

V.Bernier-Villamor, D.A.Sampson, M.J.Matunis, C.D.Lima.

ABSTRACT

E2 enzymes catalyze attachment of ubiquitin and ubiquitin-like proteins to lysine residues directly or through E3-mediated reactions. The small ubiquitin-like modifier SUMO regulates nuclear transport, stress response, and signal transduction in eukaryotes and is essential for cell-cycle progression in yeast. In contrast to most ubiquitin conjugation, the SUMO E2 enzyme Ubc9 is sufficient for substrate recognition and lysine modification of known SUMO targets. Crystallographic analysis of a complex between mammalian Ubc9 and a C-terminal domain of RanGAP1 at 2.5 A reveals structural determinants for recognition of consensus SUMO modification sequences found within SUMO-conjugated proteins. Structure-based mutagenesis and biochemical analysis of Ubc9 and RanGAP1 reveal distinct motifs required for substrate binding and SUMO modification of p53, IkappaBalpha, and RanGAP1.

Selected figure(s)

Figure 3.
Figure 3. Ribbon and Stereo Diagrams for Ubc9-RanGAP1.(A and B) Orthogonal ribbon representations with helices lettered and strands numbered, as in Figure 2. Ubc9 Cys93 and RanGAP1 Leu525, Lys526, and Glu528 are in solid bonds. N and C termini are denoted in italics.(C) Stereo image of the complex, as in (A).

Figure 5.
Figure 5. Models for Ubc9 Surfaces Utilized in Substrate, SUMO, E2, and E3 Binding(A) Surface and bond representations for Ubc9 and the RanGAP1 SUMO tetrapeptide motif, respectively. Ubc9 Asp127 (red), Cys93 (green), and Tyr87 (pink) are indicated on the Ubc9 surface. The location of the channel discussed in the text is indicated by a yellow arrow.(B) Orthogonal view of (A). RanGAP1 Lys526 Nε atom is visible beyond the yellow arrow.(C–E) Orthogonal Ubc9 surface representations in complex with RanGAP1, Mms2, E6AP, and Cbl. The RanGAP1 SUMO motif is represented by solid bonds, RanGAP1(420–589)p as a red worm, the Cbl ring finger as a light blue worm, the E6AP Hect domain as a dark blue worm, and Mms2 as a green worm. Surface area buried in respective complexes is shown as a red surface (RanGAP1), a green surface (Mms2), and a blue surface (E6AP and Cbl, combined). E2s from each complex were aligned to Ubc9 by least-squares minimization on Cα atoms. Figure 5 and Figure 7 were prepared with GRASP (Nicholls et al., 1991).

The above figures are reprinted by permission from Cell Press: Cell (2002, 108, 345-356) copyright 2002.

Figures were selected by an automated process.