1FF9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   APO SACCHAROPINE REDUCTASE

Authors :   E. Johansson, J. J. Steffens, Y. Lindqvist, G. Schneider

Date :   25 Jul 00 (Deposition) - 08 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Lysine Biosynthesis, Alpha-Aminoadipate Pathway, Saccharopine Reductase, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Johansson, J. J. Steffens, Y. Lindqvist, G. Schneider
Crystal Structure Of Saccharopine Reductase From Magnaporthe Grisea, An Enzyme Of The Alpha-Aminoadipate Pathway Of Lysine Biosynthesis.
Structure Fold. Des. V. 8 1037 2000
PubMed-ID: 11080625 | Reference-DOI: 10.1016/S0969-2126(00)00512-8
(for further references see the PDB file header)

Molecule 1 - SACCHAROPINE REDUCTASE
	Chains	:	A
	EC Number	:	1.5.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	FM5/PDB45
	Expression System Taxid	:	562
	Organism Scientific	:	MAGNAPORTHE GRISEA
	Organism Taxid	:	148305

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:156 , GLY A:157 , TRP A:174 , ARG A:247 , HOH A:563 , HOH A:673	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	SER A:11 , CYS A:33 , ARG A:34 , THR A:35 , SER A:38	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	LYS A:68 , HIS A:81 , ALA A:82 , SER A:102 , ALA A:104 , MET A:105 , HOH A:567 , HOH A:645	BINDING SITE FOR RESIDUE SO4 A 503

(no "SS Bond" information available for 1FF9)

Asymmetric Unit

No.	Residues
1	Asp A:126	-	Pro A:127

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LYS9_MAGO7_001 *	E	140	G	LYS9_MAGO7	---	---	A	E	140	G
2	UniProt	VAR_LYS9_MAGO7_002 *	L	398	F	LYS9_MAGO7	---	---	A	L	398	F
	* ID not provided by source

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

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LYS9_MAGO7_001 *	E	140	G	LYS9_MAGO7	---	---	A	E	140	G
2	UniProt	VAR_LYS9_MAGO7_002 *	L	398	F	LYS9_MAGO7	---	---	A	L	398	F
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1FF9)

(no "Exon" information available for 1FF9)

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:447
 aligned with LYS9_MAGO7 | Q9P4R4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:449
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441         
           LYS9_MAGO7     2 ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKLSAGVQHSTPISLDVNDDAALDAEVAKHDLVISLIPYTFHATVIKSAIRQKKHVVTTSYVSPAMMELDQAAKDAGITVMNEIGLDPGIDHLYAIKTIEEVHAAGGKIKTFLSYCGGLPAPESSDNPLGYKFSWSSRGVLLALRNAASFYKDGKVTNVAGPELMATAKPYFIYPGFAFVAYPNRDSTPYKERYQIPEADNIVRGTLRYQGFPQFIKVLVDIGFLSDEEQPFLKEAIPWKEATQKIVKASSASEQDIVSTIVSNATFESTEEQKRIVAGLKWLGIFSDKKITPRGNALDTLCATLEEKMQFEEGERDLVMLQHKFEIENKDGSRETRTSSLCEYGAPIGSGGYSAMAKLVGVPCAVAVKFVLDGTISDRGVLAPMNSKINDPLMKELKEKYGIECKEKVVA 450
               SCOP domains d1ff9a1 A:2-124,A:392-450 Saccharopine reductase                                                                           d1ff9a2 A:125-391 Saccharopine reductase                                                                                                                                                                                                                                   d1ff9a1 A:2-124,A:392-450 Saccharopine reductase            SCOP domains
               CATH domains 1ff9A01 A:2-124,A:395-442 NAD(P)-binding Rossmann-like Domain                                                              1ff9A02 A:125-249,A:350-394,A:443-450 Dihydrodipicolinate Reductase; domain 2                                                1ff9A03 A:250-349 Domain 3, Saccharopine reductase                                                  1ff9A02 A:125-249,A:350-394,A:443-450        1ff9A01 A:2-124,A:395-442                       1ff9A02  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhh......eeeee....hhhhhhhhhh...eeee...--hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh..........hhhhhhhhh...eeeee..eeeee.hhhhhhh.ee........eeeee.....hhhhhh......eeeeeeeee.hhhhhhhhhhhh.......hhhhh...hhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.......eeeeeeeeeeee.....eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F---------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ff9 A   2 ATKSVLMLGSGFVTRPTLDVLTDSGIKVTVACRTLESAKKLSAGVQHSTPISLDVNDDAALDAEVAKHDLVISLIP--FHATVIKSAIRQKKHVVTTSYVSPAMMELDQAAKDAGITVMNEIGLDPGIDHLYAIKTIEEVHAAGGKIKTFLSYCGGLPAPESSDNPLGYKFSWSSRGVLLALRNAASFYKDGKVTNVAGPELMATAKPYFIYPGFAFVAYPNRDSTPYKERYQIPEADNIVRGTLRYQGFPQFIKVLVDIGFLSDEEQPFLKEAIPWKEATQKIVKASSASEQDIVSTIVSNATFESTEEQKRIVAGLKWLGIFSDKKITPRGNALDTLCATLEEKMQFEEGERDLVMLQHKFEIENKDGSRETRTSSLCEYGAPIGSGGYSAMAKLVGVPCAVAVKFVLDGTISDRGVLAPMNSKINDPLMKELKEKYGIECKEKVVA 450
                                    11        21        31        41        51        61        71     |  81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441         
                                                                                                      77 80

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 '\|'

(no "Pfam Domain" information available for 1FF9)

Asymmetric Unit(hide GO term definitions)

Chain A (LYS9_MAGO7 | Q9P4R4)

molecular function
	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.
	GO:0004755	saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity	Catalysis of the reaction: L-saccharopine + H(2)O + NADP(+) = L-allysine + L-glutamate + H(+) + NADPH.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0019878	lysine biosynthetic process via aminoadipic acid	The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric 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
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:126 - Pro A:127	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	1ff9
		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
	LYS9_MAGO7 \| Q9P4R4
		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)
	1.5.1.7
		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
	LYS9_MAGO7 \| Q9P4R4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LYS9_MAGO7 \| Q9P4R4	:	1e5l 1e5q

(no "Related Entries Specified in the PDB File" available for 1FF9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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