3RQ2 - JenaLib

Title :   CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH NADH

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 :   1.80

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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	AMP A:278 , HOH A:296 , HOH A:297 , HOH A:318 , HOH A:319	BINDING SITE FOR RESIDUE MG A 277
2	AC2	SOFTWARE	ALA A:20 , SER A:22 , LYS A:24 , HIS A:149 , LYS A:186 , GLY A:187 , THR A:190 , ASN A:206 , GLY A:207 , LEU A:209 , ALA A:210 , THR A:214 , GLY A:215 , LEU A:218 , HIS A:243 , MG A:277 , HOH A:287 , HOH A:290 , HOH A:296 , HOH A:297 , HOH A:315 , HOH A:327 , HOH A:330 , HOH A:357 , HOH A:377	BINDING SITE FOR RESIDUE AMP A 278
3	AC3	SOFTWARE	HIS A:23 , LYS A:24 , MET A:39 , GLY A:41 , ALA A:42 , LYS A:57 , PRO A:75 , GLU A:76 , ALA A:77 , THR A:78 , PRO A:103 , GLY A:104 , ALA A:129 , HIS A:149 , PRO A:150 , GLY A:151 , VAL A:161 , ASP A:216 , HOH A:285 , HOH A:289 , HOH A:297 , HOH A:303 , HOH A:315 , HOH A:319 , HOH A:332 , HOH A:341 , HOH A:345 , HOH A:377 , HOH A:378 , HOH A:409 , HOH A:442 , HOH A:445	BINDING SITE FOR RESIDUE NAX A 279

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

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 d3rq2a_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.......hhhhh.eeeee......hhhhhhhhhhhhh....eeeeee...hhhhhh......eeeehhhhhh..........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
                 3rq2 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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.

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	Ligands, Modified Residues, Ions
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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rq2)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3rq2
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	4.2.1.93
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