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(-) Description

Title :  CRYSTAL STRUCTURE OF A FORMYLTETRAHYDROFOLATE DEFORMYLASE (PURU, PP_1943) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Jun 10  (Deposition) - 28 Jul 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  N-Terminal Act Domain, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Formyltetrahydrofolate Deformylase (Puru, Pp_1943) From Pseudomonas Putida Kt2440 At 2. 05 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FORMYLTETRAHYDROFOLATE DEFORMYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURU-3, PP1943, PP_1943
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 34)

Asymmetric/Biological Unit (6, 34)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2FLC2Ligand/IonCITRATE ANION
3IMD4Ligand/IonIMIDAZOLE
4MSE16Mod. Amino AcidSELENOMETHIONINE
5NA3Ligand/IonSODIUM ION
6UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:244 , ASP A:249 , HOH A:375 , HOH A:524 , HOH A:564 , HOH C:307BINDING SITE FOR RESIDUE NA A 287
02AC2SOFTWAREPHE A:97 , MSE A:174 , HIS A:194 , LYS A:204 , PRO A:205 , TYR A:206 , HIS A:207 , VAL A:251 , HOH A:352 , HOH A:487BINDING SITE FOR RESIDUE FLC A 289
03AC3SOFTWAREPRO A:83 , ARG A:84 , LEU A:270 , ASP A:272 , HOH A:409 , HOH A:735BINDING SITE FOR RESIDUE EDO A 290
04AC4SOFTWAREASN A:123 , HIS A:124 , MSE A:174 , GLN A:175 , HOH A:311BINDING SITE FOR RESIDUE IMD A 291
05AC5SOFTWAREGLU B:112 , HOH B:348 , HOH B:349 , ARG D:255BINDING SITE FOR RESIDUE EDO B 287
06AC6SOFTWARELYS B:74 , GLN B:155 , HOH B:313 , HOH B:375BINDING SITE FOR RESIDUE EDO B 288
07AC7SOFTWAREARG B:82 , PRO B:83 , ASP B:86 , LYS B:88BINDING SITE FOR RESIDUE EDO B 289
08AC8SOFTWAREASN B:123 , HIS B:124 , MSE B:174 , GLN B:175 , HOH B:323BINDING SITE FOR RESIDUE IMD B 290
09AC9SOFTWARELYS C:96 , ASP C:98 , ALA C:128 , LEU C:129 , HOH C:322 , HOH C:573BINDING SITE FOR RESIDUE NA C 287
10BC1SOFTWAREASN A:30 , SER C:154 , LYS C:157 , HOH C:402BINDING SITE FOR RESIDUE EDO C 288
11BC2SOFTWAREASN C:123 , HIS C:124 , MSE C:174 , GLN C:175 , HOH C:358BINDING SITE FOR RESIDUE IMD C 289
12BC3SOFTWAREHOH B:451 , ARG D:244 , ASP D:249 , HOH D:371 , HOH D:382 , HOH D:752BINDING SITE FOR RESIDUE NA D 287
13BC4SOFTWAREPHE D:97 , ARG D:172 , HIS D:194 , LYS D:204 , PRO D:205 , TYR D:206 , HIS D:207 , VAL D:251 , HOH D:332 , HOH D:379BINDING SITE FOR RESIDUE FLC D 289
14BC5SOFTWAREARG D:82 , PRO D:83 , LEU D:270 , ASP D:272 , HOH D:325 , HOH D:358BINDING SITE FOR RESIDUE EDO D 290
15BC6SOFTWAREHOH C:382 , PRO D:198 , LYS D:201BINDING SITE FOR RESIDUE EDO D 291
16BC7SOFTWAREASN D:123 , HIS D:124 , MSE D:174 , GLN D:175 , HOH D:364 , HOH D:714BINDING SITE FOR RESIDUE IMD D 292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NRB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:197 -Pro A:198
2Leu B:197 -Pro B:198
3Leu C:197 -Pro C:198
4Leu D:197 -Pro D:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NRB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NRB)

(-) Exons   (0, 0)

(no "Exon" information available for 3NRB)

(-) 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:281
 aligned with Q88LI9_PSEPK | Q88LI9 from UniProtKB/TrEMBL  Length:286

    Alignment length:284
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    
         Q88LI9_PSEPK     3 KNNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVIMVSKFDHCLGDLLYRHRLGELDMEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYMQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeee...---hhhhhhhhhhhhhhh.eeeeee.....eeeeee...hhhhhhhhhhhhh.....eeeeeee..hhhhh.........eee...hhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhh..eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nrb A   3 KNNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFmRVSVEIPV---NDFNSAFGKVVEKYNAEWWFRPRTDRKKVVImVSKFDHCLGDLLYRHRLGELDmEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYmQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
                                    12        22        32        42       |52     |  62        72        82        92|      102       112  |    122       132       142       152       162       172 |     182       192       202       212       222       232       242       252       262       272       282    
                                                                          50-MSE  58  62                             93-MSE               115-MSE                                                    174-MSE                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q88LI9_PSEPK | Q88LI9 from UniProtKB/TrEMBL  Length:286

    Alignment length:282
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284  
         Q88LI9_PSEPK     5 NQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVIMVSKFDHCLGDLLYRHRLGELDMEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYMQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhh.eeeeee....eeeeeee...hhhhhhhhhhhhh....eeeeeeee..hhhhh.........eee...hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhh..eeeee..........hhhhhhhhhh..eeeeeeee.....--..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nrb B   5 NQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFmRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVImVSKFDHCLGDLLYRHRLGELDmEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYmQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADL--GPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
                                    14        24        34        44     |  54        64        74        84        94       104       114|      124       134       144       154       164       174       184       194       204       214       224   |  |234       244       254       264       274       284  
                                                                        50-MSE                                     93-MSE               115-MSE                                                    174-MSE                                               228  |                                                       
                                                                                                                                                                                                                                                            231                                                       


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with Q88LI9_PSEPK | Q88LI9 from UniProtKB/TrEMBL  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
         Q88LI9_PSEPK     4 NNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVIMVSKFDHCLGDLLYRHRLGELDMEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYMQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee...hhhhhhhhhhhhh....eeeeeeee..hhhhh.........eee...hhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhh..eeeee..........hhhhhhhhhh..eeeeeeee...-.....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nrb C   4 NNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFmRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVImVSKFDHCLGDLLYRHRLGELDmEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYmQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTA-LDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
                                    13        23        33        43      | 53        63        73        83        93       103       113 |     123       133       143       153       163       173|      183       193       203       213       223  | |  233       243       253       263       273       283   
                                                                         50-MSE                                     93-MSE               115-MSE                                                    174-MSE                                             226 |                                                          
                                                                                                                                                                                                                                                          228                                                          


Chain D from PDB  Type:PROTEIN  Length:283
 aligned with Q88LI9_PSEPK | Q88LI9 from UniProtKB/TrEMBL  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
         Q88LI9_PSEPK     4 NNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVIMVSKFDHCLGDLLYRHRLGELDMEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYMQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---ACT-3nrbD01 D:7-61                                     --------------------------Formyl_trans_N-3nrbD05 D:88-266                                                                                                                                                    -------------------- Pfam domains (1)
           Pfam domains (2) ---ACT-3nrbD02 D:7-61                                     --------------------------Formyl_trans_N-3nrbD06 D:88-266                                                                                                                                                    -------------------- Pfam domains (2)
           Pfam domains (3) ---ACT-3nrbD03 D:7-61                                     --------------------------Formyl_trans_N-3nrbD07 D:88-266                                                                                                                                                    -------------------- Pfam domains (3)
           Pfam domains (4) ---ACT-3nrbD04 D:7-61                                     --------------------------Formyl_trans_N-3nrbD08 D:88-266                                                                                                                                                    -------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeee.....eeeeee...hhhhhhhhhhhhh.....eeeeeee..hhhhh.........eee...hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhh..eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nrb D   4 NNQYVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFFmRVSVEIPVAGVNDFNSAFGKVVEKYNAEWWFRPRTDRKKVVImVSKFDHCLGDLLYRHRLGELDmEVVGIISNHPREALSVSLVGDIPFHYLPVTPATKAAQESQIKNIVTQSQADLIVLARYmQILSDDLSAFLSGRCINIHHSFLPGFKGAKPYHQAHTRGVKLIGATAHFVTADLDEGPIIAQDVEHVSHRDSAEDLVRKGRDIERRVLSRAVLLFLEDRLIVNGERTVVFAD 286
                                    13        23        33        43      | 53        63        73        83        93       103       113 |     123       133       143       153       163       173|      183       193       203       213       223       233       243       253       263       273       283   
                                                                         50-MSE                                     93-MSE               115-MSE                                                    174-MSE
   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 3NRB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NRB)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: ACT (34)
(-)
Clan: no clan defined [family: Formyl_trans_N] (25)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q88LI9_PSEPK | Q88LI9)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0008864    formyltetrahydrofolate deformylase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + formate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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).
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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    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.

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