2DWC - JenaLib

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Title :   CRYSTAL STRUCTURE OF PROBABLE PHOSPHORIBOSYLGLYCINAMIDE FORMYL TRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3 COMPLEXED WITH ADP

Authors :   S. Yoshikawa, R. Arai, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama, Rik Structural Genomics/Proteomics Initiative (Rsgi)

Date :   10 Aug 06 (Deposition) - 10 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Purine Ribonucleotide Biosynthesis, Phosphoribosylglycinamide Formyltransferase, Purt, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Yoshikawa, R. Arai, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama
Crystal Structure Of Probable Phosphoribosylglycinamide Formyl Transferase From Pyrococcus Horikoshii Ot3 Complexed With Adp
To Be Published
PubMed: search

Molecule 1 - 433AA LONG HYPOTHETICAL PHOSPHORIBOSYLGLYCINAMIDE FORMYL TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)-CODONPLUS-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH0318
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	PH0318

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:378 , TYR B:382 , ARG B:385 , HOH B:982 , HOH B:1200	BINDING SITE FOR RESIDUE SO4 B 601
2	AC2	SOFTWARE	ARG A:414 , TRP A:420 , HOH A:942	BINDING SITE FOR RESIDUE SO4 A 602
3	AC3	SOFTWARE	ARG B:414 , TRP B:420 , HOH B:904 , HOH B:1004	BINDING SITE FOR RESIDUE SO4 B 603
4	AC4	SOFTWARE	LYS A:378 , TYR A:382 , ARG A:385 , HOH A:1074	BINDING SITE FOR RESIDUE SO4 A 604
5	AC5	SOFTWARE	ARG A:121 , HIS A:160 , LYS A:162 , GLU A:202 , GLU A:203 , HIS A:204 , ILE A:205 , PHE A:207 , GLU A:210 , GLN A:237 , PHE A:281 , ASN A:290 , GLU A:291	BINDING SITE FOR RESIDUE ADP A 501
6	AC6	SOFTWARE	ARG B:121 , HIS B:160 , LYS B:162 , GLU B:202 , GLU B:203 , HIS B:204 , ILE B:205 , PHE B:207 , GLU B:210 , GLN B:237 , PHE B:281 , ASN B:290 , GLU B:291 , HOH B:1003	BINDING SITE FOR RESIDUE ADP B 502

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

Asymmetric Unit

No.	Residues
1	Val A:109	-	Pro A:110
2	Tyr A:157	-	Pro A:158
3	Gln A:247	-	Pro A:248
4	Val B:109	-	Pro B:110
5	Tyr B:157	-	Pro B:158
6	Gln B:247	-	Pro B:248

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

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

(no "Exon" information available for 2DWC)

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:406
 aligned with PURT_PYRHO | O58056 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:421
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                  
                              |      8        18        28        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       318       328       338       348       358       368       378       388       398       408       418 
           PURT_PYRHO     - --MIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAIMSSSGKGSYFVKGPEDIPKAWEEAKTKARGSAEKIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHD 419
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dwcA01 A:2-131  [code=3.40.50.20, no name defined]                                                                               2dwcA02 A:132-203 ATP-grasp fold,       A domain                        2dwcA03 A:204-422 ATP-grasp fold, B domain                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.........eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeee..------.eee.hhhhhhhhhhh---------..eeeee.....eeeee..eeee.....eeeeee..eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeeee...hhhhhhhhhhh....hhhhhhhhhhhh.....eee..eeee.....eeeeeee....ee..eeehhhhhh....eeeee....ee....eeeeeeee..hhhhhhhhhhhhhhh.eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwc A   2 VVMIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAIM------SYFVKGPEDIPKAWEE---------EKIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHD 422
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |     -|      181     |   -     | 201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421 
                                                                                                                                                                                             165    172            187       197

Chain B from PDB  Type:PROTEIN  Length:409
 aligned with PURT_PYRHO | O58056 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:422
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                   
                              |      8        18        28        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       318       328       338       348       358       368       378       388       398       408       418  
           PURT_PYRHO     - --MIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAIMSSSGKGSYFVKGPEDIPKAWEEAKTKARGSAEKIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHDQ 420
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dwcB01 B:2-131  [code=3.40.50.20, no name defined]                                                                               2dwcB02 B:132-203 ATP-grasp fold, A     domain                          2dwcB03 B:204-423 ATP-grasp fold, B domain                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.........eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeee...----..eee.hhhhhhhhhh.---------..eeeee.....eeeee..eeee.....eeeeee..eeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeeee...hhhhhhhhhhh....hhhhhhhhhhhh.....eee..eeee.....eeeeeee....ee..eeehhhhhh....eeeee....ee....eeeeeeee..hhhhhhhhhhhhhhh.eee......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwc B   2 VVMIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAIMS----GSYFVKGPEDIPKAWEE---------EKIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHDQ 423
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    |  171       181     |   -     | 201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421  
                                                                                                                                                                                              166  171             187       197

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 '\|'

(no "SCOP Domain" information available for 2DWC)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PURT_PYRHO | O58056)

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:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0043815	phosphoribosylglycinamide formyltransferase 2 activity	Catalysis of the reaction: formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + diphosphate.
	GO:0004644	phosphoribosylglycinamide formyltransferase activity	Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
	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:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009152	purine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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	Cis Peptide Bonds
		Gln A:247 - Pro A:248	[ RasMol ]
		Gln B:247 - Pro B:248	[ RasMol ]
		Tyr A:157 - Pro A:158	[ RasMol ]
		Tyr B:157 - Pro B:158	[ RasMol ]
		Val A:109 - Pro A:110	[ RasMol ]
		Val B:109 - Pro B:110	[ RasMol ]

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	2dwc
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	2.1.2.-
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UniProtKB/Swiss-Prot
	PURT_PYRHO \| O58056	:	2czg

2czg	THE SAME PROTEIN, APO-FORM. RELATED ID: PHO001000318.2 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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