2QTR - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE ADENYLYLTRANSFERASE

Authors :   V. C. Sershon, B. D. Santarsiero, A. D. Mesecar

Date :   02 Aug 07 (Deposition) - 15 Jul 08 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)

Keywords :   Nad, Nucleotidyltransferase, Pyridine Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. C. Sershon, B. D. Santarsiero, A. D. Mesecar
Kinetic And X-Ray Structural Evidence For Negative Cooperativity In Substrate Binding To Nicotinate Mononucleotide Adenylyltransferase (Nmat) From Bacillus Anthracis.
J. Mol. Biol. V. 385 867 2009
PubMed-ID: 18977360 | Reference-DOI: 10.1016/J.JMB.2008.10.037

Molecule 1 - NICOTINATE (NICOTINAMIDE) NUCLEOTIDE ADENYLYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.7.7.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE)3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NADD
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392
	Strain	:	STERNE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	NXX	3	Ligand/Ion	1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	NXX	2	Ligand/Ion	1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	NXX	2	Ligand/Ion	1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:45 , ARG B:48 , SER B:156 , ARG B:160 , HOH B:215	BINDING SITE FOR RESIDUE SO4 B 190
2	AC2	SOFTWARE	HIS A:15 , HIS A:18 , ARG A:133 , SER A:155 , SER A:156 , HOH A:223 , HOH A:231 , HOH A:259	BINDING SITE FOR RESIDUE SO4 A 190
3	AC3	SOFTWARE	HIS C:15 , HIS C:18 , ARG C:133 , SER C:155 , SER C:156 , HOH C:200 , HOH C:203 , HOH C:217	BINDING SITE FOR RESIDUE SO4 C 190
4	AC4	SOFTWARE	HIS B:15 , HIS B:18 , ARG B:133 , SER B:155 , SER B:156 , HOH B:226	BINDING SITE FOR RESIDUE SO4 B 191
5	AC5	SOFTWARE	GLY B:8 , GLY B:9 , THR B:10 , PHE B:11 , HIS B:15 , HIS B:18 , ILE B:21 , ASN B:39 , PRO B:43 , LYS B:45 , TYR B:84 , THR B:85 , PHE B:103 , ILE B:104 , ILE B:105 , GLY B:106 , ASP B:108 , MET B:109 , TRP B:116 , TYR B:117 , ALA B:132 , ARG B:133 , PHE B:152 , HOH B:193 , HOH B:194 , HOH B:196 , HOH B:197 , HOH B:203 , HOH B:209 , HOH B:215 , HOH B:237 , HOH B:261 , HOH B:300	BINDING SITE FOR RESIDUE NXX B 192
6	AC6	SOFTWARE	GLY A:8 , GLY A:9 , THR A:10 , PHE A:11 , HIS A:15 , HIS A:18 , ASN A:39 , PRO A:43 , HIS A:44 , SER A:83 , TYR A:84 , THR A:85 , ILE A:105 , GLY A:106 , ASP A:108 , MET A:109 , TRP A:116 , TYR A:117 , ARG A:133 , PHE A:152 , HOH A:195 , HOH A:198 , HOH A:200 , HOH A:202 , HOH A:225 , HOH A:231 , HOH A:236 , HOH A:238 , HOH A:239 , HOH A:259 , HOH A:275	BINDING SITE FOR RESIDUE NXX A 191
7	AC7	SOFTWARE	GLY C:8 , GLY C:9 , THR C:10 , PHE C:11 , HIS C:15 , HIS C:18 , ASN C:39 , PRO C:43 , HIS C:44 , LYS C:45 , SER C:83 , TYR C:84 , THR C:85 , ILE C:105 , GLY C:106 , ASP C:108 , MET C:109 , TRP C:116 , TYR C:117 , ARG C:133 , PHE C:152 , HOH C:192 , HOH C:193 , HOH C:198 , HOH C:199 , HOH C:200 , HOH C:202 , HOH C:206 , HOH C:210 , HOH C:217 , HOH C:298	BINDING SITE FOR RESIDUE NXX C 191

(no "SS Bond" information available for 2QTR)

Asymmetric Unit

No.	Residues
1	Asp A:12	-	Pro A:13
2	Asp B:12	-	Pro B:13
3	Gly B:81	-	Pro B:82
4	Asp C:12	-	Pro C:13

(no "SAP(SNP)/Variant" information available for 2QTR)

(no "PROSITE Motif" information available for 2QTR)

(no "Exon" information available for 2QTR)

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:189
 aligned with NADD_BACAC | C3L5T6 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           NADD_BACAC     1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
               SCOP domains d2qtra_ A: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh....eee..hhhhh....hhhhhhhhhhhhh...eeeeeeehhhhhhhhhh.hhhhhh...eeeee.............eee.......hhhhhhhhhhh........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qtr A   1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with NADD_BACAC | C3L5T6 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           NADD_BACAC     1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
               SCOP domains d2qtrb_ B: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhh..eeeeeeeehhhhhhhhhh.hhhhhh...eeeee.............eee.......hhhhhhhhhhh........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qtr B   1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:189
 aligned with NADD_BACAC | C3L5T6 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           NADD_BACAC     1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
               SCOP domains d2qtrc_ C: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhh..eeeeeeeehhhhhhhhhh.hhhhhh...eeeee.............eee.......hhhhhhhhhhh........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qtr C   1 MRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Adenylyltransferase (56)

Protein domain: Nicotinamide mononucleotide (NMN) adenylyltransferase (22)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (4)

1a	d2qtra_	A:
1b	d2qtrb_	B:
1c	d2qtrc_	C:

(no "CATH Domain" information available for 2QTR)

(no "Pfam Domain" information available for 2QTR)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NADD_BACAC | C3L5T6)

molecular function
	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:0004515	nicotinate-nucleotide adenylyltransferase activity	Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-NAD+.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:12 - Pro A:13	[ RasMol ]
		Asp B:12 - Pro B:13	[ RasMol ]
		Asp C:12 - Pro C:13	[ RasMol ]
		Gly B:81 - Pro B:82	[ RasMol ]

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	2qtr
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	2.7.7.18
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	NADD_BACAC \| C3L5T6	:	3mla 3mlb 3mmx

2qtm	APO STRUCTURE
2qtn	NAMN BOUND STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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