1DJL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF HUMAN TRANSHYDROGENASE DOMAIN III WITH BOUND NADP

Authors :   S. A. White, S. J. Peak, N. P. Cotton, J. B. Jackson

Date :   03 Dec 99 (Deposition) - 06 Dec 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Rossmann Fold Dinucleotide Binding Fold Reverse Binding Of Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. White, S. J. Peake, S. Mcsweeney, G. Leonard, N. P. Cotton, J. B. Jackson
The High-Resolution Structure Of The Nadp(H)-Binding Component (Diii) Of Proton-Translocating Transhydrogenase From Human Heart Mitochondria.
Structure Fold. Des. V. 8 1 2000
PubMed-ID: 10673423 | Reference-DOI: 10.1016/S0969-2126(00)00075-7
(for further references see the PDB file header)

Molecule 1 - TRANSHYDROGENASE DIII
	Chains	:	A, B
	EC Number	:	1.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET11C
	Fragment	:	RESIDUES 837-1086
	Organ	:	HEART
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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	GOL	2	Ligand/Ion	GLYCEROL
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:6 , ARG A:1000	BINDING SITE FOR RESIDUE SO4 A 1138
2	AC2	SOFTWARE	HOH B:43 , ARG B:1000	BINDING SITE FOR RESIDUE SO4 B 2138
3	AC3	SOFTWARE	HOH A:6 , HOH A:9 , HOH A:54 , HOH A:62 , HOH A:80 , GLY A:889 , TYR A:890 , GLY A:891 , ALA A:895 , VAL A:922 , ALA A:923 , GLY A:924 , ARG A:925 , MET A:926 , PRO A:927 , GLY A:964 , ALA A:965 , ASN A:966 , ASP A:967 , THR A:968 , ALA A:982 , GLY A:983 , MET A:984 , LYS A:999 , ARG A:1000 , SER A:1001 , VAL A:1004 , GLY A:1005 , TYR A:1006 , ASP A:1025 , ALA A:1026 , GOL A:1137	BINDING SITE FOR RESIDUE NAP A 1136
4	AC4	SOFTWARE	HOH B:31 , HOH B:40 , HOH B:43 , GLY B:889 , TYR B:890 , GLY B:891 , ALA B:895 , VAL B:922 , ALA B:923 , GLY B:924 , ARG B:925 , MET B:926 , PRO B:927 , GLY B:964 , ALA B:965 , ASN B:966 , ASP B:967 , THR B:968 , LYS B:999 , ARG B:1000 , SER B:1001 , VAL B:1004 , GLY B:1005 , TYR B:1006 , GLY B:1024 , ASP B:1025 , ALA B:1026 , GOL B:2137	BINDING SITE FOR RESIDUE NAP B 2136
5	AC5	SOFTWARE	HIS A:920 , VAL A:922 , ASP A:967 , ILE A:981 , PRO A:985 , VAL A:986 , NAP A:1136	BINDING SITE FOR RESIDUE GOL A 1137
6	AC6	SOFTWARE	HIS B:920 , ASP B:967 , ILE B:981 , MET B:984 , VAL B:986 , NAP B:2136	BINDING SITE FOR RESIDUE GOL B 2137

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

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

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068789	L	977	P	NNTM_HUMAN	Disease (GCCD4)	387907233	A/B	L	934	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A/B	A	965	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A/B	N	966	K

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

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

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000344920	2a	ENSE00002080482	chr5:43603229-43603396	168	NNTM_HUMAN	-	0	0	-	-
1.3	ENST00000344920	3	ENSE00001148802	chr5:43609245-43609448	204	NNTM_HUMAN	1-51	51	0	-	-
1.4a	ENST00000344920	4a	ENSE00001174952	chr5:43613010-43613239	230	NNTM_HUMAN	51-127	77	0	-	-
1.5c	ENST00000344920	5c	ENSE00001174942	chr5:43615950-43616167	218	NNTM_HUMAN	128-200	73	0	-	-
1.6b	ENST00000344920	6b	ENSE00000742787	chr5:43619134-43619221	88	NNTM_HUMAN	200-229	30	0	-	-
1.7	ENST00000344920	7	ENSE00000742788	chr5:43624134-43624222	89	NNTM_HUMAN	230-259	30	0	-	-
1.8	ENST00000344920	8	ENSE00000742789	chr5:43628302-43628489	188	NNTM_HUMAN	259-322	64	0	-	-
1.9	ENST00000344920	9	ENSE00000742790	chr5:43644294-43644427	134	NNTM_HUMAN	322-366	45	0	-	-
1.10a	ENST00000344920	10a	ENSE00000742791	chr5:43644713-43644904	192	NNTM_HUMAN	367-430	64	0	-	-
1.11a	ENST00000344920	11a	ENSE00000742792	chr5:43645459-43645612	154	NNTM_HUMAN	431-482	52	0	-	-
1.13	ENST00000344920	13	ENSE00000742794	chr5:43649249-43649410	162	NNTM_HUMAN	482-536	55	0	-	-
1.14	ENST00000344920	14	ENSE00000742796	chr5:43650579-43650689	111	NNTM_HUMAN	536-573	38	0	-	-
1.15a	ENST00000344920	15a	ENSE00000742797	chr5:43651841-43651986	146	NNTM_HUMAN	573-621	49	0	-	-
1.16a	ENST00000344920	16a	ENSE00000742798	chr5:43653120-43653315	196	NNTM_HUMAN	622-687	66	0	-	-
1.17	ENST00000344920	17	ENSE00000742799	chr5:43655942-43656175	234	NNTM_HUMAN	687-765	79	0	-	-
1.18	ENST00000344920	18	ENSE00000742800	chr5:43656755-43656915	161	NNTM_HUMAN	765-818	54	0	-	-
1.19	ENST00000344920	19	ENSE00000742801	chr5:43659273-43659452	180	NNTM_HUMAN	819-878	60	0	-	-
1.20	ENST00000344920	20	ENSE00000742804	chr5:43675613-43675772	160	NNTM_HUMAN	879-932	54	2	A:859-889 B:859-889	31 31
1.21a	ENST00000344920	21a	ENSE00000742805	chr5:43677827-43677908	82	NNTM_HUMAN	932-959	28	2	A:889-916 B:889-916	28 28
1.22	ENST00000344920	22	ENSE00000742806	chr5:43700221-43700339	119	NNTM_HUMAN	959-999	41	2	A:916-956 B:916-956	41 41
1.23	ENST00000344920	23	ENSE00000742807	chr5:43702723-43702838	116	NNTM_HUMAN	999-1037	39	2	A:956-994 B:956-994	39 39
1.24b	ENST00000344920	24b	ENSE00001374370	chr5:43704357-43705334	978	NNTM_HUMAN	1038-1086	49	2	A:995-1040 B:995-1040	46 46

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:182
 aligned with NNTM_HUMAN | Q13423 from UniProtKB/Swiss-Prot  Length:1086

    Alignment length:182
                                   911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081  
          NNTM_HUMAN    902 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES 1083
               SCOP domains d1djla_ A: Transhydrogenase domain III (dIII)                                                                                                                                          SCOP domains
               CATH domains 1djlA00 A:859-1040 TPP-binding domain                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eeehhhhhhhhhhh.eeeee..hhhhhhhhhhh...........hhhhh.eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------P------------------------------PK-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20  PDB: A:859-889      --------------------------Exon 1.22  PDB: A:916-956                --------------------------------------Exon 1.24b  PDB: A:995-1040 UniProt: 1038-1086 Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.21a  PDB: A:889-916  ---------------------------------------Exon 1.23  PDB: A:956-994              ---------------------------------------------- Transcript 1 (2)
                1djl A  859 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES 1040
                                   868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with NNTM_HUMAN | Q13423 from UniProtKB/Swiss-Prot  Length:1086

    Alignment length:182
                                   911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081  
          NNTM_HUMAN    902 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES 1083
               SCOP domains d1djlb_ B: Transhydrogenase domain III (dIII)                                                                                                                                          SCOP domains
               CATH domains 1djlB00 B:859-1040 TPP-binding domain                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh..hhh.eeehhhhhhhhhhh.eeeee..hhhhhhhhhhh...........hhhhh.eeeeee...........hhhhhh..eeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------P------------------------------PK-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20  PDB: B:859-889      --------------------------Exon 1.22  PDB: B:916-956                --------------------------------------Exon 1.24b  PDB: B:995-1040 UniProt: 1038-1086 Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.21a  PDB: B:889-916  ---------------------------------------Exon 1.23  PDB: B:956-994              ---------------------------------------------- Transcript 1 (2)
                1djl B  859 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES 1040
                                   868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038

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) (23833)

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: Transhydrogenase domain III (dIII) (22)

Protein domain: Transhydrogenase domain III (dIII) (19)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1djla_	A:
1b	d1djlb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Human (Homo sapiens) (9)

1a	1djlA00	A:859-1040
1b	1djlB00	B:859-1040

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NNTM_HUMAN | Q13423)

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:0008750	NAD(P)+ transhydrogenase (AB-specific) activity	Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD+ and B-specific (i.e. the pro-S hydrogen is transferred) with respect to NADP+.
	GO:0003957	NAD(P)+ transhydrogenase (B-specific) activity	Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+, driving the transfer of a solute or solutes from one side of a membrane to the other. In the course of the reaction (left to right) one H atom is transferred from inside the cell to outside. The reaction is B-specific (i.e. the pro-S hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to both NAD+ and NADP+.
	GO:0008746	NAD(P)+ transhydrogenase activity	Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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:0006740	NADPH regeneration	A metabolic process that generates a pool of NADPH by the reduction of NADP+.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	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:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	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: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:0005746	mitochondrial respiratory chain	The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.
	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
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	Cis Peptide Bonds
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(no "Related Entries Specified in the PDB File" available for 1DJL)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (5, 10)

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