2VP8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RV1207

Authors :   M. Gengenbacher, T. Xu, P. Niyomwattanakit, G. Spraggon, T. Dick

Date :   27 Feb 08 (Deposition) - 12 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.64

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dihydropteroate Synthase, Mycobacterium Tuberculosis, Rv1207, Transferase, Folate Biosynthesis, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Gengenbacher, T. Xu, P. Niyomwattanakit, G. Spraggon, T. Dick
Biochemical And Structural Characterization Of The Putative Dihydropteroate Synthase Ortholog Rv1207 Of Mycobacterium Tuberculosis.
Fems Microbiol. Lett. V. 287 128 2008
PubMed-ID: 18680522 | Reference-DOI: 10.1111/J.1574-6968.2008.01302.X
(for further references see the PDB file header)

Molecule 1 - DIHYDROPTEROATE SYNTHASE 2
	Chains	:	A, B
	EC Number	:	2.1.5.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 2-318
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	DHPS 2, DIHYDROPTEROATE PYROPHOSPHORYLASE 2, MYCOBACTERIUM TUBERCULOSIS RV1207

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:211 , GLY B:243 , TRP B:244	BINDING SITE FOR RESIDUE EDO B1311
2	AC2	SOFTWARE	ARG A:211 , THR A:242 , TRP A:244	BINDING SITE FOR RESIDUE EDO A1312
3	AC3	SOFTWARE	ARG B:68	BINDING SITE FOR RESIDUE EDO A1313
4	AC4	SOFTWARE	ASP B:64	BINDING SITE FOR RESIDUE EDO A1314

(no "SS Bond" information available for 2VP8)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:27	-	Gly A:28
2	Tyr B:182	-	Gly B:183

(no "SAP(SNP)/Variant" information available for 2VP8)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTERIN_BINDING	PS50972	Pterin-binding domain profile.	DHPS2_MYCTO	42-299	2	A:42-299 B:42-299
1	PTERIN_BINDING	PS50972	Pterin-binding domain profile.	DHPS2_MYCTU	42-299	2	A:42-299 B:42-299
2	DHPS_1	PS00792	Dihydropteroate synthase signature 1.	DHPS2_MYCTO	44-59	2	A:44-49 B:44-51
2	DHPS_1	PS00792	Dihydropteroate synthase signature 1.	DHPS2_MYCTU	44-59	2	A:44-49 B:44-51
3	DHPS_2	PS00793	Dihydropteroate synthase signature 2.	DHPS2_MYCTO	78-91	2	A:78-85 B:78-86
3	DHPS_2	PS00793	Dihydropteroate synthase signature 2.	DHPS2_MYCTU	78-91	2	A:78-85 B:78-86

(no "Exon" information available for 2VP8)

Asymmetric/Biological 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:233
 aligned with DHPS2_MYCTO | P9WNC8 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:285
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
          DHPS2_MYCTO    27 AGHSTLCGRPVAGDRALIMAIVNRTPDSFYDKGATFSDAAARDAVHRAVADGADVIDVGGVKAGPGERVDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHTGGALPRTRPFRVSYGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSNKDVVGETLGVDLTERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPPT 311
               SCOP domains d2vp8a_ A: automated ma              tches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee.--------------hhhhhhhhhhhhhh...eeee.----------hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhh.eeeee..-------------...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.....ee...---------------hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PTERIN_BINDING  PDB: A:42-299 UniProt: 42-299                                                                                                                                                                                                                     ------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------DHPS_1          ------------------DHPS_2        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vp8 A  27 AGHSTLCGRPVAGDRALIMAIVN--------------DAAARDAVHRAVADGADVIDVG----------DVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHT-------------YGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALS---------------RLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPPT 311
                                    36        46  |      -       |66        76        |-        96       106       116       126       136       146       156       166 |       -     | 186       196       206       216       226       236       246    |    -         -|      276       286       296       306     
                                                 49             64                   85         96                                                                     168           182                                                                  251             267

Chain A from PDB  Type:PROTEIN  Length:233
 aligned with DHPS2_MYCTU | P9WNC9 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:285
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
          DHPS2_MYCTU    27 AGHSTLCGRPVAGDRALIMAIVNRTPDSFYDKGATFSDAAARDAVHRAVADGADVIDVGGVKAGPGERVDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHTGGALPRTRPFRVSYGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSNKDVVGETLGVDLTERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPPT 311
               SCOP domains d2vp8a_ A: automated ma              tches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee.--------------hhhhhhhhhhhhhh...eeee.----------hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhh.eeeee..-------------...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.....ee...---------------hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------PTERIN_BINDING  PDB: A:42-299 UniProt: 42-299                                                                                                                                                                                                                     ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------DHPS_1          ------------------DHPS_2        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vp8 A  27 AGHSTLCGRPVAGDRALIMAIVN--------------DAAARDAVHRAVADGADVIDVG----------DVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHT-------------YGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALS---------------RLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPPT 311
                                    36        46  |      -       |66        76        |-        96       106       116       126       136       146       156       166 |       -     | 186       196       206       216       226       236       246    |    -         -|      276       286       296       306     
                                                 49             64                   85         96                                                                     168           182                                                                  251             267

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with DHPS2_MYCTO | P9WNC8 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:282
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308  
          DHPS2_MYCTO    29 HSTLCGRPVAGDRALIMAIVNRTPDSFYDKGATFSDAAARDAVHRAVADGADVIDVGGVKAGPGERVDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHTGGALPRTRPFRVSYGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSNKDVVGETLGVDLTERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPP 310
               SCOP domains d2vp8b_ B: automated ma            tches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------Pteri            n_bind-2vp8B01 B:47-252                                                                                                                                                                                   --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------Pteri            n_bind-2vp8B02 B:47-252                                                                                                                                                                                   --------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee..eee.....eeeeeee..------------hhhhhhhhhhhhhh...eeeee.--------..hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eee........hhhhhhhhhh.eeeee..-------------...hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee........hhhhhhhhhhhhhhhhh....ee....-------------hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------PTERIN_BINDING  PDB: B:42-299 UniProt: 42-299                                                                                                                                                                                                                     ----------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ---------------DHPS_1          ------------------DHPS_2        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vp8 B  29 HSTLCGRPVAGDRALIMAIVNRT------------DAAARDAVHRAVADGADVIDVGG--------VDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHT-------------YGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSN-------------ERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPP 310
                                    38        48  |      -     |  68        78       | -      | 98       108       118       128       138       148       158       168         -   |   188       198       208       218       228       238       248   |     -       268       278       288       298       308  
                                                 51           64                    86       95                                                                      168           182                                                                   252           266

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with DHPS2_MYCTU | P9WNC9 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:282
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308  
          DHPS2_MYCTU    29 HSTLCGRPVAGDRALIMAIVNRTPDSFYDKGATFSDAAARDAVHRAVADGADVIDVGGVKAGPGERVDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHTGGALPRTRPFRVSYGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSNKDVVGETLGVDLTERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPP 310
               SCOP domains d2vp8b_ B: automated ma            tches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------Pteri            n_bind-2vp8B01 B:47-252                                                                                                                                                                                   --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------Pteri            n_bind-2vp8B02 B:47-252                                                                                                                                                                                   --------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee..eee.....eeeeeee..------------hhhhhhhhhhhhhh...eeeee.--------..hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eee........hhhhhhhhhh.eeeee..-------------...hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee........hhhhhhhhhhhhhhhhh....ee....-------------hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------PTERIN_BINDING  PDB: B:42-299 UniProt: 42-299                                                                                                                                                                                                                     ----------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ---------------DHPS_1          ------------------DHPS_2        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vp8 B  29 HSTLCGRPVAGDRALIMAIVNRT------------DAAARDAVHRAVADGADVIDVGG--------VDVDTEITRLVPFIEWLRGAYPDQLISVDTWRAQVAKAACAAGADLINDTWGGVDPAMPEVAAEFGAGLVCAHT-------------YGTTTRGVVDAVISQVTAAAERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADLVMTGWPVLMALSN-------------ERLEGTLAATALAAAAGARMFRVHEVAATRRVLEMVASIQGVRPP 310
                                    38        48  |      -     |  68        78       | -      | 98       108       118       128       138       148       158       168         -   |   188       198       208       218       228       238       248   |     -       268       278       288       298       308  
                                                 51           64                    86       95                                                                      168           182                                                                   252           266

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Dihydropteroate synthetase-like (59)

Family: automated matches (3)

Protein domain: automated matches (3)

Mycobacterium tuberculosis [TaxId: 83332] (1)

1a	d2vp8a_	A:
1b	d2vp8b_	B:

(no "CATH Domain" information available for 2VP8)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Pterin_bind (18)

Mycobacterium tuberculosis (1)

1a	Pterin_bind-2vp8B01	B:47-252
1b	Pterin_bind-2vp8B02	B:47-252

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHPS2_MYCTO | P9WNC8)

molecular function
	GO:0004156	dihydropteroate synthase activity	Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
biological process
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	GO:0042558	pteridine-containing compound metabolic process	The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.

Chain A,B (DHPS2_MYCTU | P9WNC9)

molecular function
	GO:0004156	dihydropteroate synthase activity	Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	GO:0042558	pteridine-containing compound metabolic process	The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:27 - Gly A:28	[ RasMol ]
		Tyr B:182 - Gly B:183	[ RasMol ]

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	2vp8
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Description

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Ligands, Modified Residues, Ions (1, 4)

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