1LPF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS AT 2.8 ANGSTROMS RESOLUTION. ANALYSIS OF REDOX AND THERMOSTABILITY PROPERTIES

Authors :   A. Mattevi, W. Hol

Date :   26 Oct 92 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Mattevi, G. Obmolova, K. H. Kalk, W. J. Van Berkel, W. G. Hol
Three-Dimensional Structure Of Lipoamide Dehydrogenase From Pseudomonas Fluorescens At 2. 8 A Resolution. Analysis Of Redox And Thermostability Properties.
J. Mol. Biol. V. 230 1200 1993
PubMed-ID: 8487301 | Reference-DOI: 10.1006/JMBI.1993.1236
(for further references see the PDB file header)

Molecule 1 - DIHYDROLIPOAMIDE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.8.1.4
	Engineered	:	YES
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	294

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:9 , GLY A:10 , GLY A:12 , PRO A:13 , GLY A:14 , GLU A:33 , LYS A:34 , TYR A:35 , GLY A:46 , THR A:47 , CYS A:48 , VAL A:51 , GLY A:52 , CYS A:53 , SER A:56 , LYS A:57 , GLY A:119 , GLY A:121 , ALA A:149 , SER A:150 , GLY A:151 , ILE A:191 , ARG A:278 , LEU A:285 , GLY A:317 , ASP A:318 , MET A:324 , LEU A:325 , ALA A:326 , HIS B:450 , PRO B:451	BINDING SITE FOR RESIDUE FAD A 480
2	AC2	SOFTWARE	HIS A:450 , PRO A:451 , ILE B:9 , GLY B:10 , GLY B:12 , PRO B:13 , GLY B:14 , GLU B:33 , LYS B:34 , GLY B:46 , THR B:47 , CYS B:48 , VAL B:51 , GLY B:52 , CYS B:53 , LYS B:57 , GLY B:119 , HIS B:120 , GLY B:121 , ALA B:149 , SER B:150 , GLY B:151 , SER B:152 , SER B:170 , ILE B:191 , ARG B:278 , LEU B:285 , GLY B:317 , ASP B:318 , MET B:324 , LEU B:325 , ALA B:326 , HIS B:327	BINDING SITE FOR RESIDUE FAD B 480

Asymmetric/Biological Unit

No.	Residues
1	A:48	-	A:53
2	B:48	-	B:53

Asymmetric/Biological Unit

No.	Residues
1	His A:359	-	Pro A:360
2	His A:450	-	Pro A:451
3	His B:359	-	Pro B:360
4	His B:450	-	Pro B:451

(no "SAP(SNP)/Variant" information available for 1LPF)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_1	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.	DLDH_PSEFL	46-56	2	A:45-55 B:45-55

(no "Exon" information available for 1LPF)

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:472
 aligned with DLDH_PSEFL | P14218 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:472
                                    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       451       461       471  
           DLDH_PSEFL     2 SQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIA 473
               SCOP domains d1lpfa1 A:1-158,A:278-348 Dihydrolipoamide dehydrogenase                                                                                                      d1lpfa2 A:159-277 Dihydrolipoamide dehydrogenase                                                                       d1lpfa1 A:1-158,A:278-348 Dihydrolipoamide dehydrogenase               d1lpfa3 A:349-472 Dihydrolipoamide dehydrogenase                                                                             SCOP domains
               CATH domains 1lpfA01 A:1-154,A:277-350  [code=3.50.50.60, no name defined]                                                                                             1lpfA02 A:155-276  [code=3.50.50.60, no name defined]                                                                     1lpfA01 A:1-154,A:277-350  [code=3.50.50.60, no name defined]             1lpfA03 A:351-472  [code=3.30.390.30, no name defined]                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee...eeeeee....eeeeeeeeeeee..eeee..............hhhhh......eeeeee...hhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh..eee...e.........eeeeeee....eeeeee..eee..eeeee........................eee...eeee..........hhhhhhhhhhhhhhh.............eeeeee.eeeeee..hhhhhh....eeeeeee...............eeeeeee.....eeeeeeee..hhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------PYRIDINE_RE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lpf A   1 SQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIA 472
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470

Chain B from PDB  Type:PROTEIN  Length:472
 aligned with DLDH_PSEFL | P14218 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:472
                                    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       451       461       471  
           DLDH_PSEFL     2 SQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIA 473
               SCOP domains d1lpfb1 B:1-158,B:278-348 Dihydrolipoamide dehydrogenase                                                                                                      d1lpfb2 B:159-277 Dihydrolipoamide dehydrogenase                                                                       d1lpfb1 B:1-158,B:278-348 Dihydrolipoamide dehydrogenase               d1lpfb3 B:349-472 Dihydrolipoamide dehydrogenase                                                                             SCOP domains
               CATH domains 1lpfB01 B:1-154,B:277-350  [code=3.50.50.60, no name defined]                                                                                             1lpfB02 B:155-276  [code=3.50.50.60, no name defined]                                                                     1lpfB01 B:1-154,B:277-350  [code=3.50.50.60, no name defined]             1lpfB03 B:351-472  [code=3.30.390.30, no name defined]                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee...eeeeee....eeeeeeeeeeee..eeee..............hhhhh......eeeeee...hhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh..eee...e.........eeeeeee....eeeeee..eee..eeeee........................eee...eeee..........hhhhhhhhhhhhhhh.............eeeeee.eeeeee..hhhhhh....eeeeeee...............eeeeeee.....eeeeeeee..hhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------PYRIDINE_RE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lpf B   1 SQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIA 472
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

Pseudomonas fluorescens. Organism_taxid: 294 (1)

1a	1lpfA03	A:351-472
1b	1lpfB03	B:351-472

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Pseudomonas fluorescens. Organism_taxid: 294 (9)

2a	1lpfA01	A:1-154,A:277-350
2b	1lpfB01	B:1-154,B:277-350
2c	1lpfA02	A:155-276
2d	1lpfB02	B:155-276

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DLDH_PSEFL | P14218)

molecular function
	GO:0004148	dihydrolipoyl dehydrogenase activity	Catalysis of the reaction: protein N6-(dihydrolipoyl)lysine + NAD+ = protein N6-(lipoyl)lysine + NADH + H+.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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:0016668	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		His A:359 - Pro A:360	[ RasMol ]
		His A:450 - Pro A:451	[ RasMol ]
		His B:359 - Pro B:360	[ RasMol ]
		His B:450 - Pro B:451	[ RasMol ]

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
	1lpf
		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
	DLDH_PSEFL \| P14218
		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)
	1.8.1.4
		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
	DLDH_PSEFL \| P14218
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1LPF)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (2, 6)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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