3RQ6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS SOAKED WITH ADP-RIBOSE

Authors :   I. A. Shumilin, M. Cymborowski, A. Joachimiak, W. Minor, Midwest Cent Structural Genomics (Mcsg)

Date :   27 Apr 11 (Deposition) - 27 Jul 11 (Release) - 09 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase, Lyase-Lyase Substrate Complex (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 - ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE
	Chains	:	A
	EC Number	:	4.2.1.93
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIPL
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU38720, YXKO
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	APR	2	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	APR	8	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:186 , APR A:278 , HOH A:298 , HOH A:309 , HOH A:360 , HOH A:371	BINDING SITE FOR RESIDUE MG A 277
2	AC2	SOFTWARE	ALA A:20 , SER A:22 , LYS A:24 , GLU A:76 , HIS A:149 , LYS A:186 , GLY A:187 , ASN A:188 , THR A:190 , ASN A:206 , GLY A:207 , LEU A:209 , ALA A:210 , GLY A:212 , GLY A:213 , THR A:214 , GLY A:215 , ASP A:216 , HIS A:243 , MG A:277 , HOH A:288 , HOH A:298 , HOH A:309 , HOH A:311 , HOH A:321 , HOH A:338 , HOH A:360 , HOH A:371 , HOH A:396 , HOH A:413 , HOH A:440	BINDING SITE FOR RESIDUE APR A 278
3	AC3	SOFTWARE	TYR A:79 , TRP A:80 , LYS A:86 , LEU A:92 , GLU A:93 , GLU A:94 , TYR A:96 , HOH A:306 , HOH A:420 , HOH A:425	BINDING SITE FOR RESIDUE APR A 279

(no "SS Bond" information available for 3RQ6)

(no "Cis Peptide Bond" information available for 3RQ6)

(no "SAP(SNP)/Variant" information available for 3RQ6)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNRD_BACSU	7-275	1	A:7-275
2	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNRD_BACSU	98-108	1	A:98-108
3	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNRD_BACSU	212-222	1	A:212-222

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNRD_BACSU	7-275	4	A:7-275
2	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNRD_BACSU	98-108	4	A:98-108
3	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNRD_BACSU	212-222	4	A:212-222

(no "Exon" information available for 3RQ6)

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:277
 aligned with NNRD_BACSU | P94368 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:277
                             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       
           NNRD_BACSU     - -MNVPFWTEEHVRATLPERDAESHKGTYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEATYWRDGWKKAADAQLEETYRAIAIGPGLPQTESVQQAVDHVLTADCPVILDAGALAKRTYPKREGPVILTPHPGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE 276
               SCOP domains d3rq6a_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.......hhhhh.eeeee......hhhhhhhhhhhhh....eeeee....hhhhhh......ee..hhhhhh..........eeee......hhhhhhhhhhhhh....eee.hhhh...........eee..hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.eeee.....eee.....eee....hhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------YJEF_C_3  PDB: A:7-275 UniProt: 7-275                                                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------YJEF_C_1   -------------------------------------------------------------------------------------------------------YJEF_C_2   ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rq6 A   0 AMNVPFWTEEHVRATLPERDAESHKGTYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEATYWRDGWKKAADAQLEETYRAIAIGPGLPQTESVQQAVDHVLTADCPVILDAGALAKRTYPKREGPVILTPHPGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE 276
                                     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

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: YjeF C-terminal domain-like (31)

Protein domain: automated matches (9)

Bacillus subtilis [TaxId: 1423] (9)

d3rq6a_

(no "CATH Domain" information available for 3RQ6)

(no "Pfam Domain" information available for 3RQ6)

Asymmetric Unit(hide GO term definitions)

Chain A (NNRD_BACSU | P94368)

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: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: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:0046496	nicotinamide nucleotide metabolic process	The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rq6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3rq6
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		Orientation in Membranes	:	OPM
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	NNRD_BACSU \| P94368
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	4.2.1.93
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	NNRD_BACSU \| P94368
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UniProtKB/Swiss-Prot
	NNRD_BACSU \| P94368	:	1kyh 3rph 3rpz 3rq2 3rq5 3rq8 3rqh 3rqq 3rqx

1kyh	APO-PROTEIN
3rpz	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH NADPH
3rq5	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH COA
3rq8	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS SOAKED WITH P1,P5- DI(ADENOSINE-5') PENTAPHOSPHATE
3rqh	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P6- DI(ADENOSINE-5') HEXAPHOSPHATE
3rqq	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P3- DI(ADENOSINE-5') TRIPHOSPHATE
3rqx	CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P4- DI(ADENOSINE-5') TETRAPHOSPHATE

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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