1X15 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF E. COLI TRANSHYDROGENASE DOMAIN I WITH BOUND NADH

Authors :   T. Johansson, C. Oswald, A. Pedersen, S. Tornroth, M. Okvist, B. G. Karlsson, J. Rydstrom, U. Krengel

Date :   31 Mar 05 (Deposition) - 13 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

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

Keywords :   Transhydrogenase, Nad(H)-Binding Domain, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Johansson, C. Oswald, A. Pedersen, S. Tornroth, M. Okvist, B. G. Karlsson, J. Rydstrom, U. Krengel
X-Ray Structure Of Domain I Of The Proton-Pumping Membrane Protein Transhydrogenase From Escherichia Coli
J. Mol. Biol. V. 352 299 2005
PubMed-ID: 16083909 | Reference-DOI: 10.1016/J.JMB.2005.07.022
(for further references see the PDB file header)

Molecule 1 - NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA
	Chains	:	A, B
	EC Number	:	1.6.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDC21
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NAD(H)-BINDING DOMAIN
	Gene	:	PNTA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	DH5ALPHA
	Synonym	:	PYRIDINE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT ALPHA, NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT ALPHA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:35 , HOH B:313 , ARG B:1120 , ILE B:1121 , SER B:1122 , GLN B:1125 , GLY B:1172 , GLY B:1174 , VAL B:1175 , ASP B:1195 , THR B:1196 , ARG B:1197 , GLU B:1238 , THR B:1255 , ALA B:1256 , LEU B:1257 , LEU B:1266	BINDING SITE FOR RESIDUE NAD B 1395

(no "SS Bond" information available for 1X15)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:1368	-	Pro A:1369
2	Trp B:1368	-	Pro B:1369

(no "SAP(SNP)/Variant" information available for 1X15)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALADH_PNT_1	PS00836	Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1.	PNTA_ECOLI	4-30	2	A:1004-1030 B:1004-1030
2	ALADH_PNT_2	PS00837	Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2.	PNTA_ECOLI	170-195	2	A:1170-1195 B:1170-1195

(no "Exon" information available for 1X15)

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:370
 aligned with PNTA_ECOLI | P07001 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:376
                                    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      
          PNTA_ECOLI      1 MRIGIPRERLTNETRVAATPKTVEQLLKLGFTVAVESGAGQLASFDDKAFVQAGAEIVEGNSVWQSEIILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPRISRAQSLDALSSMANIAGYRAIVEAAHEFGRFFTGQITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLELDFKEEAGSGDGYAKVMSDAFIKAEMELFAAQAKEVDIIVTTALIPGKPAPKLITREMVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKVIGYTDLPGRLPTQSSQLYGTNLVNLLKLLCKEKDGNITVDFDDVVIRGVTVIRAGEITWPAPPIQVS  376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x15A01 A:1001-1136,A:1319-1376  [code=3.40.50.1770, no name defined]                                                                   1x15A02 A:1137-1318 NAD(P)-binding Rossmann-like Domain                                                                                                                               1x15A01 A:1001-1136,A:1319-1376                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.............hhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhh.eeehhhhhhh..eee.....hhhhhh......eeee..hhhhhhhhhhhhhh...eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee..eee...eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.....------.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhhhhh.....eeee.hhhhh..........eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhheeee..ee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ALADH_PNT_1 UniProt: 4-30  -------------------------------------------------------------------------------------------------------------------------------------------ALADH_PNT_2               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1x15 A 1001 GRIGIPRERLTNETRVAATPKTVEQLLKLGFTVAVESGAGQLASFDDKAFVQAGAEIVEGNSVWQSEIILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPRISRAQSLDALSSMANIAGYRAIVEAAHEFGRFFTGQITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLELDF------GDGYAKVMSDAFIKAEMELFAAQAKEVDIIVTTALIPGKPAPKLITREMVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKVIGYTDLPGRLPTQSSQLYGTNLVNLLKLLCKEKDGNITVDFDDVVIRGVTVIRAGEITWPAPPIQVS 1376
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210     |   -  |   1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      
                                                                                                                                                                                                                                                1216   1223

Chain B from PDB  Type:PROTEIN  Length:360
 aligned with PNTA_ECOLI | P07001 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:375
                             1                                                                                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369     
          PNTA_ECOLI      - -MRIGIPRERLTNETRVAATPKTVEQLLKLGFTVAVESGAGQLASFDDKAFVQAGAEIVEGNSVWQSEIILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPRISRAQSLDALSSMANIAGYRAIVEAAHEFGRFFTGQITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLELDFKEEAGSGDGYAKVMSDAFIKAEMELFAAQAKEVDIIVTTALIPGKPAPKLITREMVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKVIGYTDLPGRLPTQSSQLYGTNLVNLLKLLCKEKDGNITVDFDDVVIRGVTVIRAGEITWPAPPIQ  374
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x15B01 B:1000-1136,B:1319-1374  [code=3.40.50.1770, no name defined]                                                                    1x15B02 B:1137-1318 NAD(P)-binding Rossmann-like Domain                                                                                                                               1x15B01 B:1000-1136,B:1319-1374                          CATH domains
           Pfam domains (1) ----AlaDh_PNT_N-1x15B01 B:1004-1137                                                                                                       --------AlaDh_PNT_C-1x15B03 B:1146-1311                                                                                                                                       --------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----AlaDh_PNT_N-1x15B02 B:1004-1137                                                                                                       --------AlaDh_PNT_C-1x15B04 B:1146-1311                                                                                                                                       --------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhh.eee.hhhhhh..eee.....hhhhhh......eeee..hhhhhhhhhhhhhhh..eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee..eee...eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee....---------------.hhhhhhhhhhhhhhhhhh.eeee.............hhhhhhh.....eeee.hhhhh..........eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhheeee..ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ALADH_PNT_1 UniProt: 4-30  -------------------------------------------------------------------------------------------------------------------------------------------ALADH_PNT_2               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1x15 B 1000 HGRIGIPRERLTNETRVAATPKTVEQLLKLGFTVAVESGAGQLASFDDKAFVQAGAEIVEGNSVWQSEIILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPRISRAQSLDALSSMANIAGYRAIVEAAHEFGRFFTGQITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLELD---------------SDAFIKAEMELFAAQAKEVDIIVTTALIPGKPAPKLITREMVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKVIGYTDLPGRLPTQSSQLYGTNLVNLLKLLCKEKDGNITVDFDDVVIRGVTVIRAGEITWPAPPIQ 1374
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209     |   -         - |    1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369     
                                                                                                                                                                                                                                                1215            1231

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 "SCOP Domain" information available for 1X15)

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: [code=3.40.50.1770, no name defined] (22)

Escherichia coli. Organism_taxid: 562. Strain: dh5alpha. (3)

1a	1x15B01	B:1000-1136,B:1319-1374
1b	1x15A01	A:1001-1136,A:1319-1376

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Escherichia coli. Organism_taxid: 562. Strain: dh5alpha. (3)

2a	1x15A02	A:1137-1318
2b	1x15B02	B:1137-1318

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Form_Glyc_dh (56)

Family: AlaDh_PNT_N (24)

Escherichia coli (strain K12) (2)

1a	AlaDh_PNT_N-1x15B01	B:1004-1137
1b	AlaDh_PNT_N-1x15B02	B:1004-1137

Clan: NADP_Rossmann (1239)

Family: AlaDh_PNT_C (25)

Escherichia coli (strain K12) (2)

2a	AlaDh_PNT_C-1x15B03	B:1146-1311
2b	AlaDh_PNT_C-1x15B04	B:1146-1311

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PNTA_ECOLI | P07001)

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: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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
	GO:0006740	NADPH regeneration	A metabolic process that generates a pool of NADPH by the reduction of NADP+.
	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.
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:0005887	integral component of plasma membrane	The component of the plasma 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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	1x15
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	PNTA_ECOLI \| P07001	:	1x13 1x14 2bru

1x13	E. COLI TRANSHYDROGENASE DOMAIN I
1x14	E. COLI TRANSHYDROGENASE DOMAIN I WITH BOUND NAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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