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(-) Description

Title :  CRYSTAL STRUCTURE OF THE L-FUCULOSE-1-PHOSPHATE ALDOLASE (AQ_1979) FROM AQUIFEX AEOLICUS VF5
 
Authors :  J. Jeyakanthan, D. Gayathri, M. Yogavel, D. Velmurugan, S. Baba, A. Ebi S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Oct 06  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (4x),B (4x)
Biol. Unit 4:  B  (4x)
Keywords :  Aldolase, Aldehyde, Enzymatic Mechanism, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, D. Gayathri, M. Yogavel, D. Velmurugan, S. Baba, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of The L-Fuculose-1-Phosphate Aldolase (Aq_1979) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ALDOLASE CLASS 2 PROTEIN AQ_1979
    Chains: A, B
    EC Number: 4.1.2.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL-21 CONDON PLUS (DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: L-FUCULOSE-1-PHOSPHATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (4x): A (4x)B (4x)
Biological Unit 4 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CL2Ligand/IonCHLORIDE ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 8)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:202BINDING SITE FOR RESIDUE CL A 1201
2AC2SOFTWARELYS B:202BINDING SITE FOR RESIDUE CL B 1202
3AC3SOFTWARETHR B:48 , SER B:50 , LEU B:63BINDING SITE FOR RESIDUE BME B 1101
4AC4SOFTWAREARG A:26 , HOH A:1286 , HOH A:1373BINDING SITE FOR RESIDUE BME A 1102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IRP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IRP)

(-) Sequences/Alignments

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:206
 aligned with MTNB_AQUAE | O67788 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
           MTNB_AQUAE     2 NVELFKKFSEKVEEIIEAGRILHSRGWVPATSGNISAKVSEEYIAITASGKHKGKLTPEDILLIDYEGRPVGGGKPSAETLLHTTVYKLFPEVNAVVHTHSPNATVISIVEKKDFVELEDYELLKAFPDIHTHEVKIKIPIFPNEQNIPLLAKEVENYFKTSEDKYGFLIRGHGLYTWGRSMEEALIHTEALEFIFECELKLLSFH 207
               SCOP domains d2irpa_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee....eeeee....hhhhhhhh.eeeee...........hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eee..hhhhhh............eeeee....hhhhhhhhhhhhhhhh.....eee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2irp A   2 NVELFKKFSEKVEEIIEAGRILHSRGWVPATSGNISAKVSEEYIAITASGKHKGKLTPEDILLIDYEGRPVGGGKPSAETLLHTTVYKLFPEVNAVVHTHSPNATVISIVEKKDFVELEDYELLKAFPDIHTHEVKIKIPIFPNEQNIPLLAKEVENYFKTSEDKYGFLIRGHGLYTWGRSmEEALIHTEALEFIFECELKLLSFH 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 |     191       201      
                                                                                                                                                                                                               183-MSE                    


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with MTNB_AQUAE | O67788 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           MTNB_AQUAE     2 NVELFKKFSEKVEEIIEAGRILHSRGWVPATSGNISAKVSEEYIAITASGKHKGKLTPEDILLIDYEGRPVGGGKPSAETLLHTTVYKLFPEVNAVVHTHSPNATVISIVEKKDFVELEDYELLKAFPDIHTHEVKIKIPIFPNEQNIPLLAKEVENYFKTSEDKYGFLIRGHGLYTWGRSMEEALIHTEALEFIFECELKLLSF 206
               SCOP domains d2irpb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee..eeeee....hhhhhhhh.eeee............hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeee.hhhhhh...........eeeeee....hhhhhhhhhhhhhh.......eee...eeeeee.hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2irp B   2 NVELFKKFSEKVEEIIEAGRILHSRGWVPATSGNISAKVSEEYIAITASGKHKGKLTPEDILLIDYEGRPVGGGKPSAETLLHTTVYKLFPEVNAVVHTHSPNATVISIVEKKDFVELEDYELLKAFPDIHTHEVKIKIPIFPNEQNIPLLAKEVENYFKTSEDKYGFLIRGHGLYTWGRSmEEALIHTEALEFIFECELKLLSF 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 |     191       201     
                                                                                                                                                                                                               183-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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MTNB_AQUAE | O67788)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0046570    methylthioribulose 1-phosphate dehydratase activity    Catalysis of the reaction: S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
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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