1LWD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA

Authors :   C. Ceccarelli, B. J. Bahnson

Date :   31 May 02 (Deposition) - 13 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Tricarboxylic Acid Cycle, Oxidoreductase, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Ceccarelli, N. B. Grodsky, N. Ariyaratne, R. F. Colman, B. J. Bahnson
Crystal Structure Of Porcine Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Complexed With Mn2+ And Isocitrate
J. Biol. Chem. V. 277 43454 2002
PubMed-ID: 12207025 | Reference-DOI: 10.1074/JBC.M207306200
(for further references see the PDB file header)

Molecule 1 - ISOCITRATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALCIDP1
	Expression System Strain	:	TB1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organ	:	HEART
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	OXALOSUCCINATE DECARBOXYLASE, IDH, NADP+-SPECIFIC ICDH, IDP, ICD-M

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ICT	2	Ligand/Ion	ISOCITRIC ACID
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:275 , ICT A:701 , HOH A:1001 , HOH A:1003 , ASP B:252	BINDING SITE FOR RESIDUE MN A 501
2	AC2	SOFTWARE	ASP A:252 , ASP B:275 , ICT B:702 , HOH B:1002 , HOH B:1004	BINDING SITE FOR RESIDUE MN B 502
3	AC3	SOFTWARE	HIS B:315 , LYS B:374 , HOH B:1565 , HOH B:1678	BINDING SITE FOR RESIDUE SO4 B 601
4	AC4	SOFTWARE	LYS A:321 , ARG A:323 , ARG B:149	BINDING SITE FOR RESIDUE SO4 B 602
5	AC5	SOFTWARE	THR A:78 , SER A:95 , ASN A:97 , ARG A:101 , ARG A:110 , ARG A:133 , TYR A:140 , ASP A:275 , MN A:501 , HOH A:1001 , HOH A:1003 , HOH A:1005 , HOH A:1283 , LYS B:212 , ASP B:252 , HOH B:1125	BINDING SITE FOR RESIDUE ICT A 701
6	AC6	SOFTWARE	LYS A:212 , ASP A:252 , THR B:78 , SER B:95 , ASN B:97 , ARG B:101 , ARG B:110 , ARG B:133 , TYR B:140 , ASP B:275 , MN B:502 , HOH B:1002 , HOH B:1004 , HOH B:1006 , HOH B:1187 , HOH B:1324	BINDING SITE FOR RESIDUE ICT B 702
7	MN1	AUTHOR	ICT A:701 , THR A:78 , SER A:95 , ASN A:97 , ARG A:101 , ARG A:110 , ARG A:133 , TYR A:140 , ASP A:275 , SER A:278 , ASP A:279 , LYS B:212 , ASP B:252 , HOH A:1001 , HOH A:1003 , HOH A:1005 , HOH B:1007 , MN A:501	ACTIVE SITE OF ISOCITRATE DEHYDROGENASE IS WHERE OXIDATIVE DECARBOXYLATION OF ISOCITRATE TAKES PLACE.
8	MN2	AUTHOR	ICT B:702 , THR B:78 , SER B:95 , ASN B:97 , ARG B:101 , ARG B:110 , ARG B:133 , TYR B:140 , ASP B:275 , SER B:278 , ASP B:279 , LYS A:212 , ASP A:252 , MN B:502 , HOH B:1002 , HOH B:1004 , HOH B:1006 , HOH A:1008	ACTIVE SITE OF ISOCITRATE DEHYDROGENASE IS WHERE OXIDATIVE DECARBOXYLATION OF ISOCITRATE TAKES PLACE.

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

(no "Cis Peptide Bond" information available for 1LWD)

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDHP_PIG	279-298	2	A:271-290 B:271-290

(no "Exon" information available for 1LWD)

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:413
 aligned with IDHP_PIG | P33198 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:413
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418   
             IDHP_PIG     9 ADQRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNRDQTNDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTFKIVFTPKDGSSAKQWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFEKHYKTDFDKYKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQTLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTSDFLDTIKSNLDRALGRQ 421
               SCOP domains d1lwda_ A: NADP-dependent isocitrate dehydrogenase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1lwdA00 A:1-413 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeeee.hhhhhhhhhhhhhhh....ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lwd A   1 ADQRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNRDQTNDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTFKIVFTPKDGSSAKQWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFEKHYKTDFDKYKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQTLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTSDFLDTIKSNLDRALGRQ 413
                                    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

Chain B from PDB  Type:PROTEIN  Length:413
 aligned with IDHP_PIG | P33198 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:413
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418   
             IDHP_PIG     9 ADQRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNRDQTNDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTFKIVFTPKDGSSAKQWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFEKHYKTDFDKYKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQTLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTSDFLDTIKSNLDRALGRQ 421
               SCOP domains d1lwdb_ B: NADP-dependent isocitrate dehydrogenase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1lwdB00 B:1-413 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) -----Iso_dh-1lwdB01 B:6-402                                                                                                                                                                                                                                                                                                                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -----Iso_dh-1lwdB02 B:6-402                                                                                                                                                                                                                                                                                                                                                                                       ----------- Pfam domains (2)
         Sec.struct. author ....ee....eeeee.hhhhhhhhhhhhhhh....ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lwd B   1 ADQRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNRDQTNDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTFKIVFTPKDGSSAKQWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFEKHYKTDFDKYKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQTLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTSDFLDTIKSNLDRALGRQ 413
                                    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

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: 3-Layer(aba) Sandwich (12045)

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Pig (Sus scrofa) (1)

1a	1lwdA00	A:1-413
1b	1lwdB00	B:1-413

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Iso_DH (49)

Family: Iso_dh (38)

Sus scrofa (Pig) (1)

1a	Iso_dh-1lwdB01	B:6-402
1b	Iso_dh-1lwdB02	B:6-402

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IDHP_PIG | P33198)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0004450	isocitrate dehydrogenase (NADP+) activity	Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0006103	2-oxoglutarate metabolic process	The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
	GO:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	GO:0006102	isocitrate metabolic process	The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
	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.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	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
		ICT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ 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 ]
		MN1	[ RasMol ]	+environment [ RasMol ]
		MN2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1lwd)

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
	1lwd
		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
	IDHP_PIG \| P33198
		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)
	1.1.1.42
		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
	IDHP_PIG \| P33198
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

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