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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE PHOSPHORIBOSYLGLYCINAMIDE FORMYL TRANSFERASE (PH0318) FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  S. Yoshikawa, R. Arai, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama, Rik Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Jul 05  (Deposition) - 13 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
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 (Ph0318) From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:378 , TYR B:382 , ARG B:385BINDING SITE FOR RESIDUE SO4 B 434
02AC2SOFTWAREARG B:414 , TRP B:420 , HOH B:506BINDING SITE FOR RESIDUE SO4 B 435
03AC3SOFTWARELYS A:378 , TYR A:382 , ARG A:385 , HOH A:520BINDING SITE FOR RESIDUE SO4 A 434
04AC4SOFTWAREARG A:414 , TRP A:420BINDING SITE FOR RESIDUE SO4 A 435
05AC5SOFTWAREHIS B:120 , ARG B:121 , GLU B:122 , ARG B:123 , ILE B:164BINDING SITE FOR RESIDUE SO4 B 436
06AC6SOFTWAREARG B:121 , ASN B:290BINDING SITE FOR RESIDUE SO4 B 437
07AC7SOFTWAREARG A:40 , GOL A:436 , HOH A:447 , ARG B:40 , PRO B:309 , GLY B:310 , HOH B:457 , HOH B:513BINDING SITE FOR RESIDUE GOL B 438
08AC8SOFTWAREGLU A:37 , THR A:303 , LEU A:304 , HIS A:307 , PRO A:308 , PRO A:309 , GLY A:310 , PHE A:311 , SER A:312 , HOH A:516 , GOL B:438BINDING SITE FOR RESIDUE GOL A 436
09AC9SOFTWAREASN A:370 , TRP A:393 , PRO B:308 , PHE B:337 , PRO B:338BINDING SITE FOR RESIDUE GOL A 437
10BC1SOFTWAREPRO A:308 , PRO A:327 , PHE A:337 , PRO A:338 , ASN B:370 , TRP B:393BINDING SITE FOR RESIDUE GOL B 439
11BC2SOFTWAREASP A:220 , TRP A:330 , ARG A:335BINDING SITE FOR RESIDUE GOL A 438
12BC3SOFTWAREVAL B:226 , THR B:227 , PHE B:229 , LYS B:264 , GLY B:333 , TYR B:334 , ARG B:335BINDING SITE FOR RESIDUE GOL B 440
13BC4SOFTWARETHR A:227 , LYS A:264 , HOH A:518 , HOH A:523 , VAL B:2BINDING SITE FOR RESIDUE GOL A 439
14BC5SOFTWAREARG A:62 , HOH A:476 , ARG B:62 , SER B:63 , TYR B:64 , ARG B:80BINDING SITE FOR RESIDUE GOL B 441
15BC6SOFTWAREASN A:53 , GOL A:441 , THR B:15 , HIS B:61 , ARG B:62 , HOH B:523BINDING SITE FOR RESIDUE GOL B 442
16BC7SOFTWAREARG A:358 , GLU B:10 , SER B:18 , GLN B:20 , HOH B:510BINDING SITE FOR RESIDUE GOL A 440
17BC8SOFTWAREARG A:62 , SER A:63 , TYR A:64 , ARG A:80 , GOL B:442BINDING SITE FOR RESIDUE GOL A 441

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CZG)

(-) Sequences/Alignments

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:405
 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 2czgA01 A:2-131  [code=3.40.50.20, no name defined]                                                                               2czgA02 A:132-203 ATP-grasp fold,       A domain                        2czgA03 A:204-423 ATP-grasp fold, B domain                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeee..------.eee..........-----------..eeeee.....eeeee..eeee.....eeeee...eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh..ee.eeeeeee..eeeeeeee...hhhhhhhhhhh....hhhhhhhhhhhh.....eee..eee......eeeeeee....ee..eeehhhhhh....eeeee....ee....eeeeeeee..hhhhhhhhhhhhhhh.eee......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czg A   2 VVMIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAIM------SYFVKGPEDIPKAW-----------EKIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHDQ 423
                                    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          185         197                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:403
 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 2czgB01 B:2-131  [code=3.40.50.20, no name defined]                                                                               2czgB02 B:132-203 ATP-grasp fold,        A domain                       2czgB03 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....hhhhhh------------.eeeee.....eeeee..eeee.....eeeeee..eeeeee..eeeeeee....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
                 2czg B   2 VVMIKLRDELGTATTDSAQKILLLGSGELGKEIAIEAQRLGVEVVAVDRYANAPAMQVAHRSYVGNMMDKDFLWSVVEREKPDAIIPEIEAINLDALFEFEKDGYFVVPNARATWIAMHRERLRETLVKEAKVPTSRYMYATTLDELYEACEKIGYPCHTKAI-------SYFVKGPEDIPKAW------------KIIVEEHIDFDVEVTELAVRHFDENGEIVTTFPKPVGHYQIDGDYHASWQPAEISEKAEREVYRIAKRITDVLGGLGIFGVEMFVKGDKVWANEVSPRPHDTGMVTLASHPPGFSEFALHLRAVLGLPIPGEWVDGYRLFPMLIPAATHVIKAKVSGYSPRFRGLVKALSVPNATVRLFGKPEAYVGRRLGIALAWDKDVEVAKRKAEMVAHMIELRTRSSDWHDQ 423
                                    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  
                                                                                                                                                                                            164     172          185          198
   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  (0, 0)

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

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological 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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        PURT_PYRHO | O58056: 2dwc

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