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Title :   CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM

Authors :   D. H. Shin, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center

Date :   14 Aug 06 (Deposition) - 29 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Nicotinate Phosphoribosyltransferase, Zin Ion, Zinc Finger Motif, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Shin, R. Kim, S. -H. Kim
Crystal Structure Of A Zinc Ion Bound Nicotinate Phosphoribosyltransferase From Thermoplasma Acidophilum
To Be Published
PubMed: search

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PB4
	Expression System Strain	:	PSJS1240
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TA1145
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	2303

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	6	Ligand/Ion	PHOSPHATE ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 66)

No.	Name	Count	Type	Full Name
1	ACY	12	Ligand/Ion	ACETIC ACID
2	MPD	12	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	36	Ligand/Ion	PHOSPHATE ION
4	TRS	6	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:24 , THR A:25 , MET A:180 , THR A:197	BINDING SITE FOR RESIDUE PO4 A 501
02	AC2	SOFTWARE	TYR A:21 , HIS A:182 , LEU A:210 , ASP A:237 , MPD A:401 , HOH A:870	BINDING SITE FOR RESIDUE PO4 A 502
03	AC3	SOFTWARE	PRO A:47 , GLY A:118 , LYS A:299 , PHE A:301 , HOH A:919	BINDING SITE FOR RESIDUE PO4 A 503
04	AC4	SOFTWARE	ARG A:243 , PHE A:246 , HOH A:862	BINDING SITE FOR RESIDUE PO4 A 504
05	AC5	SOFTWARE	CYS A:333 , HIS A:334	BINDING SITE FOR RESIDUE PO4 A 505
06	AC6	SOFTWARE	ARG A:329 , THR A:331 , HIS A:334 , GLU A:370 , TYR A:387 , HOH A:865 , HOH A:887	BINDING SITE FOR RESIDUE PO4 A 506
07	AC7	SOFTWARE	CYS A:330 , CYS A:333 , CYS A:350	BINDING SITE FOR RESIDUE ZN A 701
08	AC8	SOFTWARE	CYS A:330 , CYS A:348 , CYS A:350 , GLY A:351 , HOH A:904	BINDING SITE FOR RESIDUE ZN A 702
09	AC9	SOFTWARE	ARG A:142 , GLY A:271 , GLY A:272 , LEU A:273 , GLY A:290 , GLY A:292 , THR A:293	BINDING SITE FOR RESIDUE TRS A 601
10	BC1	SOFTWARE	TYR A:21 , PHE A:138 , THR A:179 , ARG A:235 , PO4 A:502 , HOH A:819	BINDING SITE FOR RESIDUE MPD A 401
11	BC2	SOFTWARE	PHE A:136 , VAL A:177 , LYS A:206 , TYR A:233 , MET A:268	BINDING SITE FOR RESIDUE MPD A 402
12	BC3	SOFTWARE	ASP A:68 , HIS A:364	BINDING SITE FOR RESIDUE ACY A 552

Asymmetric Unit

No.	Residues
1	A:33	-	A:100

(no "Cis Peptide Bond" information available for 2I1O)

(no "SAP(SNP)/Variant" information available for 2I1O)

(no "PROSITE Motif" information available for 2I1O)

(no "Exon" information available for 2I1O)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:389
 aligned with PNCB_THEAC | Q9HJ28 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:389
                                    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         
           PNCB_THEAC     1 MNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFK 389
               SCOP domains d2i1oa1 A:1-119 Nicotinate phosphoribosyltransferase Ta1145                                                            d2i1oa2 A:120-389 Nicotinate phosphoribosyltransferase Ta1145                                                                                                                                                                                                                  SCOP domains
               CATH domains 2i1oA01 A:1-110  [code=3.90.1170.20, no name defined]                                                         2i1oA02 A:111-300 Aldolase class I                                                                                                                                                            ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh.....hhhhhhhhhhhhhhhh.eeeeeeee.......ee..hhhhhhhhhh....eeee.....ee..........eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eee.....hhhhhhhhhhh......eeee..hhhhh.hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeeehhhhhh.....eeeeeeee..ee..........eeeeee.....eeeee....ee.......eee..eeeee..ee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i1o A   1 MNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFK 389
                                    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

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

2i1oA02

A:111-300

Architecture: Alpha-Beta Complex (3881)

Topology: Aldehyde Oxidoreductase; domain 3 (111)

Homologous Superfamily: [code=3.90.1170.20, no name defined] (12)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

2i1oA01

A:1-110

(no "Pfam Domain" information available for 2I1O)

Asymmetric Unit(hide GO term definitions)

Chain A (PNCB_THEAC | Q9HJ28)

molecular function
	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:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004514	nicotinate-nucleotide diphosphorylase (carboxylating) activity	Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
	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: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.
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
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: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.

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	PNCB_THEAC \| Q9HJ28	:	1ytd 1yte 1ytk

1ytd	CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM, NATIVE STRUCTURE
1yte	CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM, PHOSPHORIBOSYLPYROPHOSPHATE BOUND STRUCTURE
1ytk	CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM WITH NICOTINATE MONONUCLEOTIDE RELATED ID: BSGCAIR30619 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (5, 13)

Sites (12, 12)

SS Bonds (1, 1)

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