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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCERALDEHYDE OXIDOREDUCTASE
 
Authors :  H. Nishimasu, S. Fushinobu, T. Wakagi
Date :  06 May 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Xanthine Oxidoreductase Family, Molybdopterin Cofactor, Flavin Adenine Dinucleotide, Iron-Sulfur Cluster, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wakagi, H. Nishimasu, M. Miyake, S. Fushinobu
Archaeal Mo-Containing Glyceraldehyde Oxidoreductase Isozymes Exhibit Diverse Substrate Specificities Through Unique Subunit Assemblies.
Plos One V. 11 47333
PubMed-ID: 26808202  |  Reference-DOI: 10.1371/JOURNAL.PONE.0147333
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE MOLYBDOPTERIN-BINDING SUBUNIT
    Chains: A
    Organism Scientific: SULFOLOBUS TOKODAII (STRAIN DSM 16993 / JCM 10545 / NBRC 100140 / 7)
    Organism Taxid: 273063
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7
 
Molecule 2 - PUTATIVE OXIDOREDUCTASE FAD-BINDING SUBUNIT
    Chains: B
    Organism Scientific: SULFOLOBUS TOKODAII (STRAIN DSM 16993 / JCM 10545 / NBRC 100140 / 7)
    Organism Taxid: 273063
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7
 
Molecule 3 - PUTATIVE OXIDOREDUCTASE IRON-SULFUR SUBUNIT
    Chains: C
    Organism Scientific: SULFOLOBUS TOKODAII (STRAIN DSM 16993 / JCM 10545 / NBRC 100140 / 7)
    Organism Taxid: 273063
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 12)

Asymmetric Unit (8, 12)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ACY1Ligand/IonACETIC ACID
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5MCN1Ligand/IonPTERIN CYTOSINE DINUCLEOTIDE
6MO1Ligand/IonMOLYBDENUM ATOM
7PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
8PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (7, 22)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2ACY2Ligand/IonACETIC ACID
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4FES4Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5MCN2Ligand/IonPTERIN CYTOSINE DINUCLEOTIDE
6MO-1Ligand/IonMOLYBDENUM ATOM
7PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
8PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:213 , ALA A:214 , PHE A:215 , ARG A:332 , HIS A:442 , GLY A:443 , GLN A:444 , ASP A:446 , ALA A:449 , TRP A:482 , GLY A:483 , SER A:484 , ARG A:485 , THR A:486 , VAL A:487 , VAL A:594 , THR A:596 , VAL A:597 , ILE A:598 , ASN A:599 , LEU A:602 , GLN A:606 , SER A:667 , LYS A:668 , GLY A:669 , ILE A:670 , GLY A:671 , GLU A:672 , MO A:802 , HOH A:943 , HOH A:1121 , HOH A:1219 , GLN C:105 , CYS C:143 , HOH C:357binding site for residue MCN A 801
02AC2SOFTWAREGLU A:672 , MCN A:801 , HOH A:913 , HOH A:1148 , HOH A:1219binding site for residue MO A 802
03AC3SOFTWARETYR A:190 , ILE A:219 , ASP A:292 , ASP A:293 , GLY A:296 , ASN A:297 , TRP A:482 , HOH A:908 , HOH A:1112binding site for residue 1PE A 803
04AC4SOFTWAREGLU A:604 , ASP A:652 , TRP A:653 , TYR A:654 , HOH A:1026 , HOH A:1037 , HOH A:1134binding site for residue PEG A 804
05AC5SOFTWAREARG B:28 , PRO B:29 , ALA B:31 , GLY B:32 , GLY B:33 , HIS B:34 , SER B:35 , LEU B:36 , HIS B:77 , ILE B:95 , GLY B:96 , VAL B:100 , GLY B:104 , THR B:105 , GLY B:108 , SER B:109 , SER B:111 , ALA B:117 , ASP B:118 , LEU B:160 , VAL B:161 , LYS B:178 , ASP B:185 , PHE B:186 , HOH B:420 , HOH B:432 , HOH B:440 , HOH B:465 , HOH B:489 , SER C:50binding site for residue FAD B 301
06AC6SOFTWARETHR B:168 , PHE B:169 , GLU B:170 , HOH B:500binding site for residue PEG B 302
07AC7SOFTWAREASP A:106 , ASN B:79binding site for residue PG4 B 303
08AC8SOFTWARESER B:81 , LYS B:82 , SER B:93 , ARG B:101binding site for residue PEG B 304
09AC9SOFTWARETYR A:92 , MET B:1 , TYR B:2 , ARG B:43binding site for residue ACY B 305
10AD1SOFTWAREGLY C:46 , CYS C:47 , SER C:50 , CYS C:52 , GLY C:53 , CYS C:55 , CYS C:67binding site for residue FES C 201
11AD2SOFTWAREGLN C:105 , CYS C:106 , GLY C:107 , CYS C:109 , CYS C:141 , ARG C:142 , CYS C:143binding site for residue FES C 202
12AD3SOFTWAREARG B:54 , ARG B:55 , ASN C:60 , GLU C:73 , ASP C:75 , GLY C:76 , HOH C:369binding site for residue PEG C 203

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:405 -A:689

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:66 -Pro A:67
2Leu A:370 -Pro A:371
3Gly A:418 -Pro A:419
4Lys A:531 -Asn A:532
5Ile A:690 -Lys A:691
6Met A:697 -Pro A:698

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZOH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZOH)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZOH)

(-) 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:701
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh....hhhhh.....eeeeeee.....eeeee.....eee.hhh...........ee.....eeeeeee.hhhhhhhhhh...eeeee.....hhhhhh.............eeeeeeeeeehhhhhhhh..eeeeeeeeeeeee........eeeee....eeeee...hhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhh..eee..hhhhhhhhh.eeeeeeeeeeeee.....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.....ee...hhhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeeeeee.....eeeee.......hhhhhhhhhhhhhhh.hhh.eeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..eee......eehhhhhhhhhhhh....eeeeeee........eeeeeeeeee.....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh......................hhhhh...eeeee................hhhhhhhhhhhhhhhhhh..........hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zoh A   1 MYIGKPIKRIEDLRLITGKGAYVDDIELPGTLFVAFVRSKYPHARIKVKKEEGIFTGEDINPGKDFPIATKETTYVGQPIAIVIAKDRYEAYDLIESVEVEYEELDYVLDPEKALEDKVKVHSGLSSNIYYHERWKGGDVEKAFKEADLTISDTLINQRVIASPLETRGALAYFDGNKLTFYSSTQSAHYLRRNLVDFLGFENIRVIQPDVGGAFGSKIIAHPEEYALAKLALMLRKPLKWVPTRTEEFISAGHGRDKKLKFEVAVKKDGTILGIRGTLIANLGAPYPDANDDESGNVKSTVRMLPGIYKIIGADIDAYAVHTNITPTQSYRGAGRPEGIYFIERIVNIVADELGIDQYEIRLKNAIDTLPYTNIFGVTYDSGNVKKLLEIGKKYYDELKKEDGCVGVSSYIEITAFGPWEVARISVKYDGKITLVTGTGPHGQGDATAFAQIAADVLELPIEKIEVRWGDTEIIEDGIGTWGSRTVTIGGSAVLLASQKLKDKLIEIGAKILNADEYKEGNVTHKKNGNKVTFNEIVKNAFKMGESLDTTAIYNVKQPPTTPYGVHLALVKVDGTGKVFVKKYVAVDDVGTVINPLLAEGQAIGGIVQGMAQALLEGAFFDENGQLLTTNFQDYPIPTAVEIPEKIDWYYEILGKSPHPTGSKGIGEAGAIAATPTIINAVEQCIKKRITKMPVKFEELV 705
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     ||524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             516|                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              521                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhh...eee....hhhhhhhh......eeee...hhhhh.eee...eeeee...hhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhh..eeeeee..eeeeeehhhheee..ee......eeeeeeee.....eeeeeee.........eeeeeeeeee..eeeeeeeeee......eehhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zoh B   1 MYPPKFGYVIPDNLNEALEFLEEHQDARPLAGGHSLIPMLKLRLIRPSYIVEIRRFSNLSYITKDGNLYKIGALTTHYNISKSSIPLLSETASNIGDPQVRNMGTIGGSISHLDPSADYPAALIAMDAKVKITSRKGDRVVNFKSFAKDMFTPDLNPGELVTEIQVPTFEGYKFSYQKLERRAGDFAIVGVALLLKLSGDVIEDVRIGLTAVNNVAVRAKGAEEELLGKRLNDEIIEKAATRAMESANPTSGSAEYKKKMVKVLTKRAIITALK 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250||     263       273    
                                                                                                                                                                                                                                                                                    251|                      
                                                                                                                                                                                                                                                                                     255                      


Chain C from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeeee..eeeeeee....hhhhhhhhh.................eeee..eeee.hhh.hhhhh..eeehhhhh......hhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zoh C   1 MKIINSDQKVKITLKINGEKYETEVEPRRLLVHVLRELGFTGVHIGCDTSNCGACTVIMNGKSVKSCTVLAVEADGAEILTVEGLAKDGKLHPIQEAFWENHALQCGYCTPGMIMEAYWLLREKPNPTEEEIREGISGNLCRCTGYQNIVKAIKAAAEKLS 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4ZOH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZOH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZOH)

(-) Gene Ontology  (8, 12)

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