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(-) Description

Title :  STRUCTURE OF THE TETRAHYDROMETHANOPTERIN DEPENDENT FORMALDEHYDE-ACTIVATING ENZYME (FAE) FROM METHYLOBACTERIUM EXTORQUENS AM1
 
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 :  2.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  A,B,C,D,E  (2x)
Keywords :  Pentamer, Beta-Alpha-Beta Left Handed Crossover, Flexible C-Terminus, 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
    Strain: AM1

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCDE
Biological Unit 2 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:44 , ASN B:1044 , ASN C:2044 , LYS C:2046 , ASN D:3044 , ASN E:4044 , LYS E:4046BINDING SITE FOR RESIDUE CA C 201
2AC2SOFTWAREHOH C:540 , GLN C:2143 , ARG E:4144BINDING SITE FOR RESIDUE NA C 202
3AC3SOFTWAREARG C:2144 , GLU C:2149 , GLN E:4143BINDING SITE FOR RESIDUE NA E 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y5Y)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric 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 1Y5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y5Y)

(-) 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:159
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRK  160
               SCOP domains d1y5ya_ A: Formaldehyde-activating enzyme, FAE                                                                                                                  SCOP domains
               CATH domains 1y5yA00 A:2-160 Formaldehyde-activating enzyme fae                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh......eee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y5y A    2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRK  160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSA  162
               SCOP domains d1y5yb_ B: Formaldehyde-activating enzyme, FAE                                                                                                                    SCOP domains
               CATH domains 1y5yB00 B:1002-1162 Formaldehyde-activating enzyme fae                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh......eee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y5y B 1002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSA 1162
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161 


Chain C from PDB  Type:PROTEIN  Length:158
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQR  159
               SCOP domains d1y5yc_ C: Formaldehyde-activating enzyme, FAE                                                                                                                 SCOP domains
               CATH domains 1y5yC00 C:2002-2159 Formaldehyde-activating enzyme fae                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh......eee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y5y C 2002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQR 2159
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151        


Chain D from PDB  Type:PROTEIN  Length:161
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSA  162
               SCOP domains d1y5yd_ D: Formaldehyde-activating enzyme, FAE                                                                                                                    SCOP domains
               CATH domains 1y5yD00 D:3002-3162 Formaldehyde-activating enzyme fae                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh......eee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y5y D 3002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSA 3162
                                  3011      3021      3031      3041      3051      3061      3071      3081      3091      3101      3111      3121      3131      3141      3151      3161 


Chain E from PDB  Type:PROTEIN  Length:158
 aligned with FAE_METEA | Q9FA38 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           FAE_METEA      2 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQR  159
               SCOP domains d1y5ye_ E: Formaldehyde-activating enzyme, FAE                                                                                                                 SCOP domains
               CATH domains 1y5yE00 E:4002-4159 Formaldehyde-activating enzyme fae                                                                                                         CATH domains
           Pfam domains (1) -------Fae-1y5yE01 E:4009-4159                                                                                                                                 Pfam domains (1)
           Pfam domains (2) -------Fae-1y5yE02 E:4009-4159                                                                                                                                 Pfam domains (2)
           Pfam domains (3) -------Fae-1y5yE03 E:4009-4159                                                                                                                                 Pfam domains (3)
           Pfam domains (4) -------Fae-1y5yE04 E:4009-4159                                                                                                                                 Pfam domains (4)
           Pfam domains (5) -------Fae-1y5yE05 E:4009-4159                                                                                                                                 Pfam domains (5)
         Sec.struct. author ......eeeeeee.hhhhheeeeeeeee..hhhhhhhhhhhhh......eee.eee..ee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y5y E 4002 AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQR 4159
                                  4011      4021      4031      4041      4051      4061      4071      4081      4091      4101      4111      4121      4131      4141      4151
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (7, 7)

Asymmetric 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: 1y60

(-) Related Entries Specified in the PDB File

1y60 THE SAME PROTEIN COMPLEXED WITH 5,10-METHYLENE TETRAHYDROMETHANOPTERIN