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(-) Description

Title :  CRYSTAL STRUCTURE OF FORMALDEHYDE DEHYDROGENASE
 
Authors :  N. Tanaka, Y. Kusakabe, K. Ito, T. Yoshimoto, K. T. Nakamura
Date :  21 Dec 01  (Deposition) - 11 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tanaka, Y. Kusakabe, K. Ito, T. Yoshimoto, K. T. Nakamura
Crystal Structure Of Formaldehyde Dehydrogenase From Pseudomonas Putida: The Structural Origin Of The Tightly Bound Cofactor In Nicotinoprotein Dehydrogenases
J. Mol. Biol. V. 324 519 2002
PubMed-ID: 12445786  |  Reference-DOI: 10.1016/S0022-2836(02)01066-5

(-) Compounds

Molecule 1 - FORMALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: GLUTATHIONE-INDEPENDENT FORMALDEHYDE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO42Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO44Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:46 , HIS A:67 , ASP A:169 , NAD A:1403 , HOH A:1404BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS A:97 , CYS A:100 , CYS A:103 , CYS A:111BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWARECYS B:46 , HIS B:67 , ASP B:169 , NAD B:2403 , HOH B:2404BINDING SITE FOR RESIDUE ZN B 1003
4AC4SOFTWARECYS B:97 , CYS B:100 , CYS B:103 , CYS B:111BINDING SITE FOR RESIDUE ZN B 1004
5AC5SOFTWAREPRO A:241 , LEU A:242 , HIS A:269 , HOH A:1548 , HOH A:1618 , HOH A:1634 , HOH A:1735 , HOH A:1836BINDING SITE FOR RESIDUE SO4 A 1003
6AC6SOFTWAREPRO B:241 , LEU B:242 , HIS B:269 , HOH B:2656 , HOH B:2667 , HOH B:2718 , HOH B:2846BINDING SITE FOR RESIDUE SO4 B 1002
7AC7SOFTWAREGLY A:47 , SER A:48 , GLN A:50 , HIS A:51 , PHE A:93 , ASP A:169 , THR A:173 , GLY A:193 , GLY A:195 , PRO A:196 , VAL A:197 , GLY A:216 , ASP A:217 , LEU A:218 , ARG A:222 , ALA A:261 , VAL A:262 , ALA A:266 , ARG A:267 , HIS A:269 , VAL A:282 , PRO A:299 , LEU A:301 , TRP A:327 , GLY A:336 , GLN A:337 , THR A:338 , PHE A:379 , ZN A:1001 , HOH A:1409 , HOH A:1415 , HOH A:1426 , HOH A:1450 , HOH A:1467 , HOH A:1579BINDING SITE FOR RESIDUE NAD A 1403
8AC8SOFTWAREGLY B:47 , SER B:48 , GLN B:50 , HIS B:51 , PHE B:93 , ASP B:169 , THR B:173 , GLY B:193 , GLY B:195 , PRO B:196 , VAL B:197 , GLY B:216 , ASP B:217 , LEU B:218 , ARG B:222 , LEU B:236 , ALA B:261 , VAL B:262 , ALA B:266 , ARG B:267 , HIS B:269 , VAL B:282 , PRO B:299 , LEU B:301 , TRP B:327 , GLY B:336 , GLN B:337 , THR B:338 , PHE B:379 , ZN B:1003 , HOH B:2404 , HOH B:2422 , HOH B:2425 , HOH B:2427 , HOH B:2482 , HOH B:2490 , HOH B:2503 , HOH B:2602 , HOH B:2670 , HOH B:2691BINDING SITE FOR RESIDUE NAD B 2403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KOL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.FADH_PSEPU67-81
 		  2A:66-80
B:66-80
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.FADH_PSEPU67-81
 		  4A:66-80
B:66-80

(-) Exons   (0, 0)

(no "Exon" information available for 1KOL)

(-) 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:396
 aligned with FADH_PSEPU | P46154 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:396
                                    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       332       342       352       362       372       382       392      
           FADH_PSEPU     3 GNRGVVYLGSGKVEVQKIDYPKMQDPRGKKIEHGVILKVVSTNICGSDQHMVRGRTTAQVGLVLGHEITGEVIEKGRDVENLQIGDLVSVPFNVACGRCRSCKEMHTGVCLTVNPARAGGAYGYVDMGDWTGGQAEYLLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNPARLAHAKAQGFEIADLSLDTPLHEQIAALLGEPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIPGLYVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAIMWDRINIAEVVGVQVISLDDAPRGYGEFDAGVPKKFVIDPHKTFSA 398
               SCOP domains d1kola1 A:2-160,A:356-397 Formaldehyde dehydrogenase                                                                                                           d1kola2 A:161-355 Formaldehyde dehydrogenase                                                                                                                                                       d1kola1 A:2-160,A:356-397                  SCOP domains
               CATH domains 1kolA01 A:2-170,A:338-397 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                          1kolA02 A:171-337 NAD(P)-binding Rossmann-like Domain                                                                                                                  1kolA01 A:2-170,A:338-397                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeee................eeeeeeeee.hhhhhhhhh..............eeeeeeee...........eee...ee....hhhhhh.hhhhh.........ee...............eeee.hhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee.....hhhhhhhhhhh.....eeee...........hhhhh...hhhhhhhhhhh....eeee............hhhhhh.....hhhhhhhh..eeee...hhhhhhhhhhhhhhh...hhhhhhheeeehhhhhhhhhhhhhhh...eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------ADH_ZINC       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kol A   2 GNRGVVYLGSGKVEVQKIDYPKMQDPRGKKIEHGVILKVVSTNICGSDQHMVRGRTTAQVGLVLGHEITGEVIEKGRDVENLQIGDLVSVPFNVACGRCRSCKEMHTGVCLTVNPARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNPARLAHAKAQGFEIADLSLDTPLHEQIAALLGEPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIPGLYVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAIMWDRINIAEVVGVQVISLDDAPRGYGEFDAGVPKKFVIDPHKTFSA 397
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391      


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with FADH_PSEPU | P46154 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:396
                                    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       332       342       352       362       372       382       392      
           FADH_PSEPU     3 GNRGVVYLGSGKVEVQKIDYPKMQDPRGKKIEHGVILKVVSTNICGSDQHMVRGRTTAQVGLVLGHEITGEVIEKGRDVENLQIGDLVSVPFNVACGRCRSCKEMHTGVCLTVNPARAGGAYGYVDMGDWTGGQAEYLLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNPARLAHAKAQGFEIADLSLDTPLHEQIAALLGEPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIPGLYVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAIMWDRINIAEVVGVQVISLDDAPRGYGEFDAGVPKKFVIDPHKTFSA 398
               SCOP domains d1kolb1 B:2-160,B:356-397 Formaldehyde dehydrogenase                                                                                                           d1kolb2 B:161-355 Formaldehyde dehydrogenase                                                                                                                                                       d1kolb1 B:2-160,B:356-397                  SCOP domains
               CATH domains 1kolB01 B:2-170,B:338-397 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                          1kolB02 B:171-337 NAD(P)-binding Rossmann-like Domain                                                                                                                  1kolB01 B:2-170,B:338-397                                    CATH domains
           Pfam domains (1) -------------------------------ADH_N-1kolB01 B:33-151                                                                                                 ---------------------AlaDh_PNT_C-1kolB03 B:173-246                                             ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------ADH_N-1kolB02 B:33-151                                                                                                 ---------------------AlaDh_PNT_C-1kolB04 B:173-246                                             ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee..eeeeeee................eeeeeeeee.hhhhhhhhh..............eeeeeeee...........eee...ee....hhhhhh.hhhhh.........ee...............eeee.hhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee.....hhhhhhhhhhh.....eeee...........hhhhh...hhhhhhhhhhh....eeee..............hhhhh....hhhhhhhh..eeee...hhhhhhhhhhhhhhh...hhhhhhheeeehhhhhhhhhhhhhh....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------ADH_ZINC       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kol B   2 GNRGVVYLGSGKVEVQKIDYPKMQDPRGKKIEHGVILKVVSTNICGSDQHMVRGRTTAQVGLVLGHEITGEVIEKGRDVENLQIGDLVSVPFNVACGRCRSCKEMHTGVCLTVNPARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYVAGAGPVGLAAAASARLLGAAVVIVGDLNPARLAHAKAQGFEIADLSLDTPLHEQIAALLGEPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIPGLYVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAIMWDRINIAEVVGVQVISLDDAPRGYGEFDAGVPKKFVIDPHKTFSA 397
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GroES (70)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FADH_PSEPU | P46154)
molecular function
    GO:0018467    formaldehyde dehydrogenase activity    Catalysis of the reaction: formaldehyde + H(2)O + NAD(+) = formate + 2 H(+) + NADH.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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