1PT9 - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE DIII COMPONENT OF TRANSHYDROGENASE WITH A THIO-NICOTINAMIDE NUCLEOTIDE ANALOGUE

Authors :   A. Singh, J. D. Venning, P. G. Quirk, G. I. Van Boxel, D. J. Rodrigues, S. J. B. Jackson

Date :   23 Jun 03 (Deposition) - 07 Oct 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (2x),B (2x)
Biol. Unit 4: A (1x),B (1x)
Biol. Unit 5: A  (2x)
Biol. Unit 6: B  (2x)

Keywords :   Transhydrogenase, Thio-Nicotinamide, Mitochondria, Proton Translocation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Singh, J. D. Venning, P. G. Quirk, G. I. Van Boxel, D. J. Rodrigues, S. A. White, J. B. Jackson
Interactions Between Transhydrogenase And Thio-Nicotinamide Analogues Of Nad(H) And Nadp(H) Underline The Importance Of Nucleotide Conformational Changes In Coupling To Proton Translocation
J. Biol. Chem. V. 278 33208 2003
PubMed-ID: 12791694 | Reference-DOI: 10.1074/JBC.M303061200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	TAP	2	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TAP	1	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TAP	1	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	TAP	2	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TAP	1	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 5 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	TAP	2	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 6 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	TAP	2	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:164 , HOH A:356 , HOH A:363	BINDING SITE FOR RESIDUE SO4 A 208
2	AC2	SOFTWARE	ARG B:164 , HOH B:338 , HOH B:362	BINDING SITE FOR RESIDUE SO4 B 210
3	AC3	SOFTWARE	GLY A:53 , TYR A:54 , GLY A:55 , VAL A:86 , ALA A:87 , GLY A:88 , ARG A:89 , MET A:90 , PRO A:91 , GLY A:128 , ALA A:129 , ASN A:130 , ASP A:131 , THR A:132 , ALA A:146 , GLY A:147 , LYS A:163 , ARG A:164 , SER A:165 , VAL A:168 , GLY A:169 , TYR A:170 , ASP A:189 , ALA A:190 , GOL A:220 , HOH A:305 , HOH A:328 , HOH A:332 , HOH A:385 , HOH A:386	BINDING SITE FOR RESIDUE TAP A 300
4	AC4	SOFTWARE	GLY B:53 , TYR B:54 , GLY B:55 , ALA B:59 , VAL B:86 , ALA B:87 , GLY B:88 , ARG B:89 , MET B:90 , PRO B:91 , GLY B:128 , ALA B:129 , ASN B:130 , ASP B:131 , THR B:132 , LYS B:163 , ARG B:164 , SER B:165 , VAL B:168 , GLY B:169 , TYR B:170 , ASP B:189 , ALA B:190 , GOL B:230 , HOH B:305 , HOH B:312 , HOH B:338 , HOH B:348 , HOH B:371	BINDING SITE FOR RESIDUE TAP B 301
5	AC5	SOFTWARE	HIS A:84 , VAL A:86 , ASP A:131 , MET A:148 , PRO A:149 , VAL A:150 , TAP A:300 , HOH A:376	BINDING SITE FOR RESIDUE GOL A 220
6	AC6	SOFTWARE	HIS B:84 , VAL B:86 , ASP B:131 , MET B:148 , VAL B:150 , TAP B:301	BINDING SITE FOR RESIDUE GOL B 230

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric 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	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A/B	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A/B	N	130	K

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

Biological Unit 1 (3, 3)

								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	L	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A	N	130	K

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

Biological Unit 2 (3, 3)

								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	B	L	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	B	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	B	N	130	K

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

Biological Unit 3 (3, 12)

								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	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A/B	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A/B	N	130	K

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

Biological Unit 4 (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	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A/B	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A/B	N	130	K

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

Biological Unit 5 (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	L	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	A	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	A	N	130	K

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

Biological Unit 6 (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	B	L	98	P
2	UniProt	VAR_068790	A	1008	P	NNTM_HUMAN	Disease (GCCD4)	387907234	B	A	129	P
3	UniProt	VAR_068791	N	1009	K	NNTM_HUMAN	Disease (GCCD4)	370273690	B	N	130	K

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

PROSITE Motifs (0, 0)

Exons (5, 10)

Sequences/Alignments

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: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 d1pt9a_ A: Transhydrogenase domain III (dIII)                                                                                                                                          SCOP domains
               CATH domains 1pt9A00 A:23-204 TPP-binding domain                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhh.hhh.eeehhhhhhhh....eeeee..hhhhhhhhhhh...........hhhhh.eeeee............hhhhhh..eee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------P------------------------------PK-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.20  PDB: A:23-53        --------------------------Exon 1.22  PDB: A:80-120 UniProt: 959-999--------------------------------------Exon 1.24b  PDB: A:159-204 UniProt: 1038-1086  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.21a  PDB: A:53-80    ---------------------------------------Exon 1.23  PDB: A:120-158              ---------------------------------------------- Transcript 1 (2)
                1pt9 A   23 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES  204
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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 d1pt9b_ B: Transhydrogenase domain III (dIII)                                                                                                                                          SCOP domains
               CATH domains 1pt9B00 B:23-204 TPP-binding domain                                                                                                                                                    CATH domains
           Pfam domains (1) PNTB-1pt9B01 B:23-201                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) PNTB-1pt9B02 B:23-201                                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhh.eeeeeehhhhhhh.hhhhhhhhhhhhhhh..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:23-53        --------------------------Exon 1.22  PDB: B:80-120 UniProt: 959-999--------------------------------------Exon 1.24b  PDB: B:159-204 UniProt: 1038-1086  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.21a  PDB: B:53-80    ---------------------------------------Exon 1.23  PDB: B:120-158              ---------------------------------------------- Transcript 1 (2)
                1pt9 B   23 PMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRES  204
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (18, 18)

Asymmetric 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.

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