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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UBC DOMAIN OF BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 6
 
Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, C. Butler-Cole, C. Bountra, J. Wei C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Struct Genomics Consortium (Sgc)
Date :  29 Feb 08  (Deposition) - 01 Apr 08  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Apoptosis, Ligase, Protease Inhibitor, Thiol Protease Inhibitor, Ubl Conjugation Pathway, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sheng, J. H. Hong, R. Doherty, T. Srikumar, J. Shloush, G. V. Avvakumov, J. R. Walker, S. Xue, D. Neculai, J. W. Wan, S. K. Kim, C. H. Arrowsmith, B. Raught, S. Dhe-Paganon
A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen.
Mol Cell Proteomics V. 11 329 2012
PubMed-ID: 22496338  |  Reference-DOI: 10.1074/MCP.O111.013706

(-) Compounds

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 6
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneBIRC6, KIAA1289
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING BIR DOMAIN ENZYME APOLLON

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3CEG)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:4785 -B:4785

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:4608 -Pro A:4609
2Tyr B:4608 -Pro B:4609

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.BIRC6_HUMAN4576-4704
 
  2A:4548-4676
B:4548-4676
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.BIRC6_HUMAN4576-4704
 
  1A:4548-4676
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.BIRC6_HUMAN4576-4704
 
  1-
B:4548-4676

(-) Exons   (0, 0)

(no "Exon" information available for 3CEG)

(-) Sequences/Alignments

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:292
 aligned with BIRC6_HUMAN | Q9NR09 from UniProtKB/Swiss-Prot  Length:4857

    Alignment length:298
                                  4530      4540      4550      4560      4570      4580      4590      4600      4610      4620      4630      4640      4650      4660      4670      4680      4690      4700      4710      4720      4730      4740      4750      4760      4770      4780      4790      4800      4810        
         BIRC6_HUMAN   4521 LKSLEEKYVAVMKKLQFDTFEMVSEDEDGKLGFKVNYHYMSQVKNANDANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDIMKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQATVKWAMLEQIRNPSPCFKEVIHKHFYLKRVEIMAQCEEWIADIQQYSSDKRVGRTMSHHAAALKRHTAQLREELLKLPCPEGLD 4818
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cegA00 A:4493-4790 Ubiquitin Conjugating Enzyme                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeee..eee.....eee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeeeee..........eeeeeee..........eeee.....................hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..------hhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------UBIQUITIN_CONJUGAT_2  PDB: A:4548-4676 UniProt: 4576-4704                                                                        ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ceg A 4493 LKSLEEKYVAVmKKLQFDTFEmVSEDEDGKLGFKVNYHYmSQVKNANDANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDImKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQATVKWAmLEQIRNPSPCFKEVIHKHFYLKRVEImAQCEEWIADIQQY------GRTmSHHAAALKRHTAQLREELLKLPCPEGLD 4790
                                  4502 |    4512 |    4522      4532      4542      4552      4562      4572      4582      4592      4602      4612      4622      4632      4642      4652      4662      4672      4682      4692      4702      4712      4722      4732      4742      4752      4762      4772      4782        
                                    4504-MSE  4514-MSE          4532-MSE                                         4581-MSE                                                                                                                           4712-MSE                   4739-MSE     4752   4759  |                            
                                                                                                                                                                                                                                                                                                      4762-MSE                        

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with BIRC6_HUMAN | Q9NR09 from UniProtKB/Swiss-Prot  Length:4857

    Alignment length:296
                                  4532      4542      4552      4562      4572      4582      4592      4602      4612      4622      4632      4642      4652      4662      4672      4682      4692      4702      4712      4722      4732      4742      4752      4762      4772      4782      4792      4802      4812      
         BIRC6_HUMAN   4523 SLEEKYVAVMKKLQFDTFEMVSEDEDGKLGFKVNYHYMSQVKNANDANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDIMKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQATVKWAMLEQIRNPSPCFKEVIHKHFYLKRVEIMAQCEEWIADIQQYSSDKRVGRTMSHHAAALKRHTAQLREELLKLPCPEGLD 4818
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cegB00 B:4495-4790 Ubiquitin Conjugating En zyme                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeee..eee.....eee.....hhhhhhh.-...hhhhhhhhhhhhhhhh..........eeeeee.....eeeeeee..........eeeeeee..........eeee.....................hhhhh...............hhhhhhhhhhhhh...hhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--.-.hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------UBIQUITIN_CONJUGAT_2  PDB: B:4548-4676 UniProt: 4576-4704                                                                        ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ceg B 4495 SLEEKYVAVmKKLQFDTFEmVSEDEDGKLGFKVNYHYmSQVKNA-DANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDImKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQATVKWAmLEQIRNPSPCFKEVIHKHFYLKRVEImAQCEEWIADIQQY--D-RVGRTmSHHAAALKRHTAQLREELLKLPCPEGLD 4790
                                  4504      4514      4524      4534   | |4544      4554      4564      4574      4584      4594      4604      4614      4624      4634      4644      4654      4664      4674      4684      4694      4704      4714      4724      4734    | 4744       | -| |   4764      4774      4784      
                                  4504-MSE  4514-MSE          4532-MSE38 |                                     4581-MSE                                                                                                                           4712-MSE                   4739-MSE     4752  | |    |                            
                                                                      4540                                                                                                                                                                                                                   4755 |    |                            
                                                                                                                                                                                                                                                                                               4757    |                            
                                                                                                                                                                                                                                                                                                    4762-MSE                        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3CEG)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BIRC6_HUMAN | Q9NR09)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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).
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0060711    labyrinthine layer development    The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0032465    regulation of cytokinesis    Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
    GO:0060712    spongiotrophoblast layer development    The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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