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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE AMINOMETHYLTRANSFERASE (YGFZ) FROM ESCHERICHIA COLI AT 1.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Aug 04  (Deposition) - 31 Aug 04  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Unknown Protein From 2D-Page (Spot Pr51) (B2898) From Escherichia Coli K12 At 1. 30 A Resolutio
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNKNOWN PROTEIN FROM 2D-PAGE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YGFZ, B2898
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SPOT PR51

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4EDO3Ligand/Ion1,2-ETHANEDIOL
5MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:27 , ARG A:74 , LEU A:162 , TRP A:189 , ASN A:193 , HOH A:527 , HOH A:558BINDING SITE FOR RESIDUE ACT A 504
2AC2SOFTWAREGLU A:286 , HOH A:585 , HOH A:587 , HOH A:655 , HOH A:752 , HOH A:832 , HOH A:875BINDING SITE FOR RESIDUE CA A 505
3AC3SOFTWARELYS A:68 , PHE A:209 , ILE A:210 , ARG A:246 , HOH A:827BINDING SITE FOR RESIDUE CL A 506
4AC4SOFTWARETHR A:23 , LEU A:24 , ASP A:25 , VAL A:116 , LEU A:117 , HOH A:568 , HOH A:661BINDING SITE FOR RESIDUE EDO A 501
5AC5SOFTWAREARG A:16 , LYS A:99 , VAL A:107 , THR A:108 , ILE A:109 , HOH A:633 , HOH A:797BINDING SITE FOR RESIDUE EDO A 502
6AC6SOFTWAREGLU A:38 , SER A:50 , GLU A:260 , HOH A:733BINDING SITE FOR RESIDUE EDO A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VLY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:156 -Pro A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VLY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VLY)

(-) Exons   (0, 0)

(no "Exon" information available for 1VLY)

(-) 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:323
 aligned with YGFZ_ECOLI | P0ADE8 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:323
                                    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       292       302       312       322   
           YGFZ_ECOLI     3 FTPFPPRQPTASARLPLTLMTLDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLE 325
               SCOP domains d1vlya2 A:3-243 Hypothetical protein YgfZ, N-terminal domain                                                                                                                                                                                     d1vlya1 A:244-325 Hypothetical protein YgfZ, C-terminal domain                     SCOP domains
               CATH domains ------------------------1vlyA02 A:27-113 Aminomethyltransferase beta-barrel domains                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------GCV_T-1vlyA01 A:21-219                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..eeee...eeeeeee..hhhhhhhh....hhhhh....eeeeeee.....eeeeeeeeee..eeeeeeehhhhhhhhhhhhh.......eeeee...eeeeee..hhhhhhhh...........eeee..eeeeee.....eeeeeehhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhh...hhhhhhhhhh...........hhhhhhhh.......eeeeeeee...........eeeee..eeeee.eeeeeee.....eeeeeeee........ee.......eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vly A   3 FTPFPPRQPTASARLPLTLmTLDDWALATITGADSEKYmQGQVTADVSQmAEDQHLLAAHCDAKGKmWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANmLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEmVARAKFRGANKRALWLLAGSASRLPEAGEDLELKmGENWRRTGTVLAAVKLEDGQVVVQVVmNNDmEPDSIFRVRDDANTLHIEPLPYSLE 325
                                    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       292   |   302       312       322   
                                              22-MSE             41-MSE     52-MSE           69-MSE                                                                                                172-MSE                                                       234-MSE                            269-MSE                    296-MSE                         
                                                                                                                                                                                                                                                                                                                                   300-MSE                     


Chain A from PDB  Type:PROTEIN  Length:323
 aligned with YGFZ_SHIFL | P0ADE9 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:323
                                    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       292       302       312       322   
           YGFZ_SHIFL     3 FTPFPPRQPTASARLPLTLMTLDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLE 325
               SCOP domains d1vlya2 A:3-243 Hypothetical protein YgfZ, N-terminal domain                                                                                                                                                                                     d1vlya1 A:244-325 Hypothetical protein YgfZ, C-terminal domain                     SCOP domains
               CATH domains ------------------------1vlyA02 A:27-113 Aminomethyltransferase beta-barrel domains                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------GCV_T-1vlyA01 A:21-219                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..eeee...eeeeeee..hhhhhhhh....hhhhh....eeeeeee.....eeeeeeeeee..eeeeeeehhhhhhhhhhhhh.......eeeee...eeeeee..hhhhhhhh...........eeee..eeeeee.....eeeeeehhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhh...hhhhhhhhhh...........hhhhhhhh.......eeeeeeee...........eeeee..eeeee.eeeeeee.....eeeeeeee........ee.......eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vly A   3 FTPFPPRQPTASARLPLTLmTLDDWALATITGADSEKYmQGQVTADVSQmAEDQHLLAAHCDAKGKmWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANmLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEmVARAKFRGANKRALWLLAGSASRLPEAGEDLELKmGENWRRTGTVLAAVKLEDGQVVVQVVmNNDmEPDSIFRVRDDANTLHIEPLPYSLE 325
                                    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       292   |   302       312       322   
                                              22-MSE             41-MSE     52-MSE           69-MSE                                                                                                172-MSE                                                       234-MSE                            269-MSE                    296-MSE                         
                                                                                                                                                                                                                                                                                                                                   300-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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: FBD (14)

(-) Gene Ontology  (6, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YGFZ_ECOLI | P0ADE8)
molecular function
    GO:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (YGFZ_SHIFL | P0ADE9)
molecular function
    GO:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        YGFZ_ECOLI | P0ADE8: 1nrk
        YGFZ_SHIFL | P0ADE9: 1nrk

(-) Related Entries Specified in the PDB File

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