2AB5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   BI3 LAGLIDADG MATURASE

Authors :   A. Longo, C. W. Leonard, G. S. Bassi, D. Berndt, J. M. Krahn, T. M. Hall, K. M. Weeks

Date :   14 Jul 05 (Deposition) - 30 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Maturase, Laglidadg Endonuclease, Group I Intron Splicing, Rna Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Longo, C. W. Leonard, G. S. Bassi, D. Berndt, J. M. Krahn, T. M. Hall, K. M. Weeks
Evolution From Dna To Rna Recognition By The Bi3 Laglidadg Maturase
Nat. Struct. Mol. Biol. V. 12 779 2005
PubMed-ID: 16116439 | Reference-DOI: 10.1038/NSMB976
(for further references see the PDB file header)

Molecule 1 - MRNA MATURASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET19B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL INSERTION OF MGHHHHH
	Gene	:	CYTOCHROME B INTRON BI3
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 31)

No.	Name	Count	Type	Full Name
1	MSE	23	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:358 , ARG B:384 , HOH B:613	BINDING SITE FOR RESIDUE SO4 B 601
2	AC2	SOFTWARE	LYS A:358 , ARG A:384 , ASN A:435 , HOH A:626	BINDING SITE FOR RESIDUE SO4 A 602
3	AC3	SOFTWARE	HIS A:296 , ILE A:297 , ARG A:298 , HOH A:720 , HOH A:726	BINDING SITE FOR RESIDUE SO4 A 603
4	AC4	SOFTWARE	GLY B:313 , LYS B:314 , ARG B:336 , ASN B:337 , HIS B:340 , HOH B:697	BINDING SITE FOR RESIDUE SO4 B 604
5	AC5	SOFTWARE	GLY A:313 , LYS A:314 , ARG A:336 , ASN A:337 , HIS A:340 , HOH A:634 , HOH A:722	BINDING SITE FOR RESIDUE SO4 A 605
6	AC6	SOFTWARE	LYS B:332 , ASN B:334 , ARG B:336	BINDING SITE FOR RESIDUE SO4 B 606
7	AC7	SOFTWARE	PHE A:511 , LYS A:512 , HOH A:609 , HOH A:738 , LYS B:285 , TYR B:286 , TYR B:375	BINDING SITE FOR RESIDUE SO4 A 607
8	AC8	SOFTWARE	LYS A:423 , LYS A:424 , MSE A:425	BINDING SITE FOR RESIDUE SO4 A 608

(no "SS Bond" information available for 2AB5)

(no "Cis Peptide Bond" information available for 2AB5)

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MBI3_YEAST_001 *	G	269	V	MBI3_YEAST	---	---	A/B	V	269	V
2	UniProt	VAR_MBI3_YEAST_002 *	D	350	N	MBI3_YEAST	---	---	A/B	N	350	N
3	UniProt	VAR_MBI3_YEAST_003 *	E	412	K	MBI3_YEAST	---	---	A/B	K	412	K
4	UniProt	VAR_MBI3_YEAST_004 *	Q	434	M	MBI3_YEAST	---	---	A/B	M	434	M
5	UniProt	VAR_MBI3_YEAST_005 *	S	437	N	MBI3_YEAST	---	---	A/B	N	437	N
6	UniProt	VAR_MBI3_YEAST_006 *	R	463	K	MBI3_YEAST	---	---	A/B	K	463	K
7	UniProt	VAR_MBI3_YEAST_007 *	G	471	D	MBI3_YEAST	---	---	A/B	D	471	D
8	UniProt	VAR_MBI3_YEAST_008 *	P	515	S	MBI3_YEAST	---	---	A/B	S	515	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2AB5)

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	Q0115	1	Q0115.1	Mito:36540-36954	415	MBI3_YEAST	1-139	139	0	-	-
1.2	Q0115	2	Q0115.2	Mito:37723-37736	14	MBI3_YEAST	139-143	5	0	-	-
1.3	Q0115	3	Q0115.3	Mito:39141-40265	1125	MBI3_YEAST	144-517	374	2	A:257-517 B:256-517 (gaps)	261 262

Asymmetric/Biological 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:261
 aligned with MBI3_YEAST | Q9ZZW7 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:261
                                   266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516 
           MBI3_YEAST   257 KLNTDNPIYAYIGGLFEGDGWITISKKGKYLLYELGIEMHIRDIQLLYKIKNILGIGKVTIKKLKMKDGTIKEMCKFNVRNKNHLKNIIIPIFDKYPMLTNKHYDYLYFKDNLLKDIKYYNDLSYYLRPIKPFNTTEDILNKNYFSSWLIGFFEAESCFSIYKPMNKKMKTASFEVSQNNSMEVMLAIKSYLKITQNIYTDKFNNSRMTTKSINGIKNVVMFINNNPIKLLGYKKLQYLLFLKDLRTITKYNNYFKIPPKY 517
               SCOP domains d2ab5a1 A:257-389 automated matches                                                                                                  d2ab5a2 A:390-517 automated matches                                                                                              SCOP domains
               CATH domains 2ab5A01 A:257-383 Homing endonucleases                                                                                         2ab5A02 A:384-517 Homing endonucleases                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhheeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhh...........hhhhhhh..hhhhhhhhhhhhheeeeee........eeeeeee...hhhhhhhhhhhh.....eeee....eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------V--------------------------------------------------------------------------------N-------------------------------------------------------------K---------------------M--N-------------------------K-------D-------------------------------------------S-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:257-517 UniProt: 144-517 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 2ab5 A 257 KLNTDNPIYAYIVGLFEGDGWITISKKGKYLLYELGIEmHIRDIQLLYKIKNILGIGKVTIKKLKmKDGTIKEmCKFNVRNKNHLKNIIIPIFNKYPmLTNKHYDYLYFKDNLLKDIKYYNDLSYYLRPIKPFNTTEDILNKNYFSSWLIGFFEAKSCFSIYKPmNKKmKTASFEVSmNNNmEVmLAIKSYLKINNNIYmNEFNNSKmTTKSINDIKNVVmFINNNPIKLLGYKKLQYLLFLKDLRTITKYNNYFKIPSKY 517
                                   266       276       286       296       306       316     | 326   |   336       346       356       366       376       386       396       406       416    |  426       436 |  |  446       456       466       476|      486       496       506       516 
                                                                295-MSE                    322-MSE 330-MSE                 354-MSE                                                            421-MSE      434-MSE  |            456-MSE 464-MSE      477-MSE                                    
                                                                                                                                                                                                  425-MSE      438-MSE                                                                           
                                                                                                                                                                                                                  441-MSE

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with MBI3_YEAST | Q9ZZW7 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:262
                                   265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515  
           MBI3_YEAST   256 HKLNTDNPIYAYIGGLFEGDGWITISKKGKYLLYELGIEMHIRDIQLLYKIKNILGIGKVTIKKLKMKDGTIKEMCKFNVRNKNHLKNIIIPIFDKYPMLTNKHYDYLYFKDNLLKDIKYYNDLSYYLRPIKPFNTTEDILNKNYFSSWLIGFFEAESCFSIYKPMNKKMKTASFEVSQNNSMEVMLAIKSYLKITQNIYTDKFNNSRMTTKSINGIKNVVMFINNNPIKLLGYKKLQYLLFLKDLRTITKYNNYFKIPPKY 517
               SCOP domains d2ab5b1 B:256-389 automated matches                                                                                                   d2ab5b2 B:390-517 automated ma     tches                                                                                         SCOP domains
               CATH domains 2ab5B01 B:256-383 Homing endonucleases                                                                                          2ab5B02 B:384-517 Homing endonucleas     es                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhheeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhh...........hhhhhhh..hhhhhhhhhhhhheeeeee.-----..eeeeeee...hhhhhhhhhhhh.....eeee....eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------V--------------------------------------------------------------------------------N-------------------------------------------------------------K---------------------M--N-------------------------K-------D-------------------------------------------S-- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: B:256-517 (gaps) UniProt: 144-517 [INCOMPLETE]                                                                                                                                                                                                          Transcript 1
                 2ab5 B 256 HKLNTDNPIYAYIVGLFEGDGWITISKKGKYLLYELGIEmHIRDIQLLYKIKNILGIGKVTIKKLKmKDGTIKEmCKFNVRNKNHLKNIIIPIFNKYPmLTNKHYDYLYFKDNLLKDIKYYNDLSYYLRPIKPFNTTEDILNKNYFSSWLIGFFEAKSCFSIYK-----mKTASFEVSmNNNmEVmLAIKSYLKINNNIYmNEFNNSKmTTKSINDIKNVVmFINNNPIKLLGYKKLQYLLFLKDLRTITKYNNYFKIPSKY 517
                                   265       275       285       295       305       315      |325    |  335       345       355       365       375       385       395       405       415   |   425       435  |  | 445       455|      465       475 |     485       495       505       515  
                                                                 295-MSE                    322-MSE 330-MSE                 354-MSE                                                          419     |      434-MSE  |            456-MSE 464-MSE      477-MSE                                    
                                                                                                                                                                                                   425-MSE      438-MSE                                                                           
                                                                                                                                                                                                                   441-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Homing endonuclease-like (42)

Superfamily: Homing endonucleases (38)

Family: automated matches (1)

Protein domain: automated matches (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d2ab5a1	A:257-389
1b	d2ab5a2	A:390-517
1c	d2ab5b1	B:256-389
1d	d2ab5b2	B:390-517

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Endonuclease I-creI (41)

Homologous Superfamily: Homing endonucleases (40)

Baker's yeast (Saccharomyces cerevisiae) (8)

1a	2ab5A02	A:384-517
1b	2ab5B02	B:384-517
1c	2ab5B01	B:256-383
1d	2ab5A01	A:257-383

(no "Pfam Domain" information available for 2AB5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MBI3_YEAST | Q9ZZW7)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0000372	Group I intron splicing	The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize).
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological 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
		MSE	[ 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 ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ab5)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	2ab5
		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
	MBI3_YEAST \| Q9ZZW7
		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)
	(no 'Enzyme Classificator' available)
		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
	MBI3_YEAST \| Q9ZZW7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2AB5)

(no "Related Entries Specified in the PDB File" available for 2AB5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 31)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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