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(-) Description

Title :  STRUCTURE OF THE TETRAHYDROMETHANOPTERIN DEPENDENT FORMALDEHYDE-ACTIVATING ENZYME (FAE) FROM METHYLOBACTERIUM EXTORQUENS AM1 WITH BOUND 5,10-METHYLENE TETRAHYDROMETHANOPTERIN
 
Authors :  P. Acharya, M. Goenrich, C. H. Hagemeier, U. Demmer, J. A. Vorholt, R. K. U. Ermler
Date :  03 Dec 04  (Deposition) - 11 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Pentamer; Beta-Alpha-Beta Left Handed Crossover; Tetrahydromethanopterin-Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Acharya, M. Goenrich, C. H. Hagemeier, U. Demmer, J. A. Vorholt, R. K. Thauer, U. Ermler
How An Enzyme Binds The C1-Carrier Tetrahydromethanopterin: Structure Of The Tetrahydromethanopterin Dependent Formaldehyde-Activating Enzyme (Fae) From Methylobacterium Extorquens Am1
J. Biol. Chem. V. 280 13712 2005
PubMed-ID: 15632161  |  Reference-DOI: 10.1074/JBC.M412320200

(-) Compounds

Molecule 1 - FORMALDEHYDE-ACTIVATING ENZYME FAE
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FAE
    Organism Scientific: METHYLOBACTERIUM EXTORQUENS
    Organism Taxid: 272630
    Other Details: COMPLEXED WITH PTERIN-RELATED COFACTOR
    Strain: AM1

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1H4M5Ligand/Ion5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH D:224 , HOH D:843 , HIS D:3022 , ASP D:3024 , LYS D:3071 , VAL D:3072 , THR D:3073 , ASN D:3075 , PHE D:3119 , HOH E:810 , LEU E:4052 , LEU E:4053 , ASP E:4076 , ALA E:4077 , ALA E:4080 , PHE E:4084 , GLN E:4088BINDING SITE FOR RESIDUE H4M D 994
2AC2SOFTWAREHOH C:483 , HIS C:2022 , ASP C:2024 , LYS C:2071 , VAL C:2072 , THR C:2073 , PHE C:2119 , PHE C:2166 , HIS D:3047 , GLY D:3048 , THR D:3050 , LEU D:3052 , LEU D:3053 , ASN D:3075 , ASP D:3076 , ALA D:3077 , PHE D:3084 , GLN D:3088BINDING SITE FOR RESIDUE H4M C 995
3AC3SOFTWARETHR A:50 , LEU A:52 , LEU A:53 , ASP A:76 , ALA A:77 , PHE A:84 , GLN A:88 , HOH A:855 , HOH E:260 , HIS E:4022 , ASP E:4024 , LYS E:4071 , VAL E:4072 , THR E:4073 , PHE E:4119BINDING SITE FOR RESIDUE H4M E 996
4AC4SOFTWAREHOH B:812 , HOH B:815 , HIS B:1022 , ASP B:1024 , LYS B:1071 , VAL B:1072 , THR B:1073 , THR C:2050 , LEU C:2052 , LEU C:2053 , ILE C:2074 , ASN C:2075 , ASP C:2076 , ALA C:2077 , ALA C:2080 , PHE C:2084 , GLN C:2088BINDING SITE FOR RESIDUE H4M B 997
5AC5SOFTWAREHIS A:22 , ASP A:24 , LYS A:71 , VAL A:72 , THR A:73 , PHE A:119 , HOH A:388 , HOH B:814 , THR B:1050 , LEU B:1052 , LEU B:1053 , VAL B:1055 , ILE B:1074 , ASN B:1075 , ASP B:1076 , ALA B:1077 , PHE B:1084 , GLN B:1088BINDING SITE FOR RESIDUE H4M B 998

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y60)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Lys A:63 -Pro A:64
2Glu A:149 -Pro A:150
3Lys B:1063 -Pro B:1064
4Glu B:1149 -Pro B:1150
5Lys C:2063 -Pro C:2064
6Glu C:2149 -Pro C:2150
7Lys D:3063 -Pro D:3064
8Glu D:3149 -Pro D:3150
9Lys E:4063 -Pro E:4064
10Glu E:4149 -Pro E:4150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y60)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y60)

(-) 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:168
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN  169
               SCOP domains d1y60a_ A: Formaldehyde-activating enzyme, FAE                                                                                                                           SCOP domains
               CATH domains 1y60A00 A:2-169 Formaldehyde-activating enzyme fae                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh.......ee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y60 A    2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN  169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN  169
               SCOP domains d1y60b_ B: Formaldehyde-activating enzyme, FAE                                                                                                                           SCOP domains
               CATH domains 1y60B00 B:1002-1169 Formaldehyde-activating enzyme fae                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh.......ee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y60 B 1002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN 1169
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161        


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN  169
               SCOP domains d1y60c_ C: Formaldehyde-activating enzyme, FAE                                                                                                                           SCOP domains
               CATH domains 1y60C00 C:2002-2169 Formaldehyde-activating enzyme fae                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh.......ee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y60 C 2002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN 2169
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161        


Chain D from PDB  Type:PROTEIN  Length:169
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAANA  170
               SCOP domains d1y60d_ D: Formaldehyde-activating enzyme, FAE                                                                                                                            SCOP domains
               CATH domains 1y60D00 D:3002-3170 Formaldehyde-activating enzyme fae                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh.......ee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y60 D 3002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAANA 3170
                                  3011      3021      3031      3041      3051      3061      3071      3081      3091      3101      3111      3121      3131      3141      3151      3161         


Chain E from PDB  Type:PROTEIN  Length:168
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN  169
               SCOP domains d1y60e_ E: Formaldehyde-activating enzyme, FAE                                                                                                                           SCOP domains
               CATH domains 1y60E00 E:4002-4169 Formaldehyde-activating enzyme fae                                                                                                                   CATH domains
           Pfam domains (1) -------Fae-1y60E01 E:4009-4168                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) -------Fae-1y60E02 E:4009-4168                                                                                                                                         - Pfam domains (2)
           Pfam domains (3) -------Fae-1y60E03 E:4009-4168                                                                                                                                         - Pfam domains (3)
           Pfam domains (4) -------Fae-1y60E04 E:4009-4168                                                                                                                                         - Pfam domains (4)
           Pfam domains (5) -------Fae-1y60E05 E:4009-4168                                                                                                                                         - Pfam domains (5)
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh.......ee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y60 E 4002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAAN 4169
                                  4011      4021      4031      4041      4051      4061      4071      4081      4091      4101      4111      4121      4131      4141      4151      4161
   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, 5)

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

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (FAE_METEA | Q9FA38)
molecular function
    GO:0016840    carbon-nitrogen lyase activity    Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH3, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99).
    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.
biological process
    GO:0016051    carbohydrate biosynthetic process    The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0046294    formaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
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
        FAE_METEA | Q9FA38: 1y5y

(-) Related Entries Specified in the PDB File

1y5y THE SAME PROTEIN, APO FORM