3RT7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF TM0922, A FUSION OF A DOMAIN OF UNKNOWN FUNCTION AND ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP-GLUCOSE

Authors :   I. A. Shumilin, M. Cymborowski, S. A. Lesley, W. Minor

Date :   03 May 11 (Deposition) - 22 Jun 11 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (8x)

Keywords :   Unknown Function, Adp/Atp-Dependent Nad(P)H-Hydrate Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. A. Shumilin, M. Cymborowski, O. Chertihin, K. N. Jha, J. C. Herr, S. A. Lesley, A. Joachimiak, W. Minor
Identification Of Unknown Protein Function Using Metabolite Cocktail Screening.
Structure V. 20 1715 2012
PubMed-ID: 22940582 | Reference-DOI: 10.1016/J.STR.2012.07.016

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A
	EC Number	:	4.2.1.93
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0922, TM_0922
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

Molecule 2 - UNKNOWN PEPTIDE, PROBABLY FROM EXPRESSION HOST
	Chains	:	B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Other Details	:	UNKNOWN PEPTIDE, PROBABLY FROM EXPRESSION HOST
	Strain	:	BL21(DE3)

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (8x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	ADQ	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	1	Ligand/Ion	POTASSIUM ION
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 32)

No.	Name	Count	Type	Full Name
1	ADQ	24	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
2	GOL	8	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:52 , ASP A:114 , PHE A:117 , VAL A:146 , VAL A:148 , SER A:150	BINDING SITE FOR RESIDUE K A 491
2	AC2	SOFTWARE	ADQ A:494 , HOH A:535 , HOH A:552 , HOH A:553	BINDING SITE FOR RESIDUE MG A 492
3	AC3	SOFTWARE	GLY A:50 , ASN A:51 , ASN A:52 , PHE A:117 , GLY A:118 , THR A:119 , GLY A:120 , ARG A:122 , GLY A:123 , GLU A:124 , TYR A:129 , LYS A:375 , HOH A:524 , HOH A:563	BINDING SITE FOR RESIDUE ADQ A 493
4	AC4	SOFTWARE	ARG A:225 , SER A:227 , LYS A:229 , HIS A:366 , LYS A:402 , SER A:403 , ALA A:404 , THR A:406 , ASN A:421 , THR A:422 , LEU A:424 , SER A:425 , LYS A:426 , GLY A:427 , GLY A:428 , SER A:429 , GLY A:430 , HIS A:458 , MG A:492 , HOH A:519 , HOH A:535 , HOH A:602	BINDING SITE FOR RESIDUE ADQ A 494
5	AC5	SOFTWARE	HIS A:228 , LYS A:229 , HIS A:366 , PRO A:367 , GLY A:368 , ARG A:372 , VAL A:378 , LYS A:382 , SER A:403 , HOH A:525	BINDING SITE FOR RESIDUE ADQ A 495
6	AC6	SOFTWARE	ASP A:5 , LEU A:19 , MET A:20 , ASP A:55 , ILE A:196 , HOH A:545	BINDING SITE FOR RESIDUE GOL A 496

(no "SS Bond" information available for 3RT7)

Asymmetric Unit

No.	Residues
1	Phe A:182	-	Pro A:183
2	Phe A:269	-	Pro A:270

(no "SAP(SNP)/Variant" information available for 3RT7)

Asymmetric Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNR_THEMA	1-204	1	A:1-204
2	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNR_THEMA	212-488	1	A:212-488
3	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNR_THEMA	311-321	1	A:311-321
4	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNR_THEMA	427-437	1	A:427-437

Biological Unit 1 (4, 32)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNR_THEMA	1-204	8	A:1-204
2	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNR_THEMA	212-488	8	A:212-488
3	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNR_THEMA	311-321	8	A:311-321
4	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNR_THEMA	427-437	8	A:427-437

(no "Exon" information available for 3RT7)

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
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Chain A from PDB  Type:PROTEIN  Length:489
 aligned with NNR_THEMA | Q9X024 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:489
                                    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       480         
            NNR_THEMA     1 MKEIDELTIKEYGVDSRILMERAGISVVLAMEEELGNLSDYRFLVLCGGGNNGGDGFVVARNLLGVVKDVLVVFLGKKKTPDCEYNYGLYKKFGGKVVEQFEPSILNEFDVVVDAIFGTGLRGEITGEYAEIINLVNKSGKVVVSVDVPSGIDSNTGKVLRTAVKADLTVTFGVPKIGHILFPGRDLTGKLKVANIGHPVHLINSINRYVITREMVRSLLPERPRDSHKGTYGKVLIIAGSRLYSGAPVLSGMGSLKVGTGLVKLAVPFPQNLIATSRFPELISVPIDTEKGFFSLQNLQECLELSKDVDVVAIGPGLGNNEHVREFVNEFLKTLEKPAVIDADAINVLDTSVLKERKSPAVLTPHPGEMARLVKKTVGDVKYNYELAEEFAKENDCVLVLKSATTIVTDGEKTLFNITGNTGLSKGGSGDVLTGMIAGFIAQGLSPLEASTVSVYLHGFAAELFEQDERGLTASELLRLIPEAIRRLK 489
               SCOP domains d3rt7a1 A:1-211 Hypothetical protein TM0922, N-terminal domain                                                                                                                                                     d3rt7a2 A:212-489 Hypothetical protein TM0922, C-terminal domain                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh...ee...hhhhhhhh.eeeee..........hhhhhhhhhhhhhh..eeeee.....................eeeee...hhhhhh.hhhhhhheeeee....hhhhhh...eee.hhhhhhhhh.......hhhhh.eeeee.......hhhhhhhhhhhhh...eeeeeee...hhhhhhhh...eeeee.......hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeehhhhhhh.hhhhhhhh...eee..hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhh.eeee....eeee....eeee...hhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) YJEF_N  PDB: A:1-204 UniProt: 1-204                                                                                                                                                                         -------YJEF_C_3  PDB: A:212-488 UniProt: 212-488                                                                                                                                                                                                                                            - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YJEF_C_1   ---------------------------------------------------------------------------------------------------------YJEF_C_2   ---------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt7 A   1 MKEIDELTIKEYGVDSRILMERAGISVVLAMEEELGNLSDYRFLVLCGGGNNGGDGFVVARNLLGVVKDVLVVFLGKKKTPDCEYNYGLYKKFGGKVVEQFEPSILNEFDVVVDAIFGTGLRGEITGEYAEIINLVNKSGKVVVSVDVPSGIDSNTGKVLRTAVKADLTVTFGVPKIGHILFPGRDLTGKLKVANIGHPVHLINSINRYVITREMVRSLLPERPRDSHKGTYGKVLIIAGSRLYSGAPVLSGMGSLKVGTGLVKLAVPFPQNLIATSRFPELISVPIDTEKGFFSLQNLQECLELSKDVDVVAIGPGLGNNEHVREFVNEFLKTLEKPAVIDADAINVLDTSVLKERKSPAVLTPHPGEMARLVKKTVGDVKYNYELAEEFAKENDCVLVLKSATTIVTDGEKTLFNITGNTGLSKGGSGDVLTGMIAGFIAQGLSPLEASTVSVYLHGFAAELFEQDERGLTASELLRLIPEAIRRLK 489
                                    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       480

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3rt7 B   1 AAWLFEA   7

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 "CATH Domain" information available for 3RT7)

(no "Pfam Domain" information available for 3RT7)

Asymmetric Unit(hide GO term definitions)

Chain A (NNR_THEMA | Q9X024)

molecular function
	GO:0052855	ADP-dependent NAD(P)H-hydrate dehydratase activity	Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H(+) + NADH + phosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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		Phe A:182 - Pro A:183	[ RasMol ]
		Phe A:269 - Pro A:270	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

Exons (0, 0)

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SCOP Domains (2, 2)

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Gene Ontology (8, 8)

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