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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEOXY-SCYLLO-INOSOSE SYNTHASE COMPLEXED WITH CARBAGLUCOSE-6-PHOSPHATE, NAD+ AND CO2+
 
Authors :  E. Nango, T. Kumasaka
Date :  25 Apr 06  (Deposition) - 08 May 07  (Release) - 29 Apr 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, 2-Deoxystreptamine, Dehydroquinate Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Nango, T. Kumasaka, T. Hirayama, N. Tanaka, T. Eguchi
Structure Of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme In The Biosynthesis Of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, In Complex With A Mechanism-Based Inhibitor And Nad+
Proteins V. 70 517 2008
PubMed-ID: 17879343  |  Reference-DOI: 10.1002/PROT.21526
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-DEOXY-SCYLLO-INOSOSE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 11)

Asymmetric/Biological Unit (7, 11)
No.NameCountTypeFull Name
1CAK1Ligand/Ion[(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE
2CO2Ligand/IonCOBALT (II) ION
3EXO1Ligand/Ion(1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PO41Ligand/IonPHOSPHATE ION
7SO32Ligand/IonSULFITE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:183 , HIS A:246 , HIS A:262 , EXO A:607 , HOH A:695BINDING SITE FOR RESIDUE CO A 601
02AC2SOFTWAREGLU A:243 , TYR A:244 , GLY A:245 , HIS A:246 , THR A:247 , ALA A:273 , MET A:335 , ILE A:336 , HOH A:721BINDING SITE FOR RESIDUE SO3 A 605
03AC3SOFTWARELYS A:141 , ASN A:151 , LYS A:322 , EXO A:607 , ARG B:119BINDING SITE FOR RESIDUE PO4 A 608
04AC4SOFTWAREGLU B:183 , HIS B:246 , HIS B:262 , CAK B:609 , HOH B:701BINDING SITE FOR RESIDUE CO B 602
05AC5SOFTWAREGLU B:243 , TYR B:244 , GLY B:245 , HIS B:246 , THR B:247 , ALA B:273 , MET B:335 , ILE B:336 , HOH B:716BINDING SITE FOR RESIDUE SO3 B 606
06AC6SOFTWAREASP A:42 , GLY A:44 , VAL A:45 , PRO A:46 , ILE A:49 , GLU A:72 , LYS A:75 , GLY A:103 , GLY A:104 , LEU A:105 , ASN A:108 , THR A:128 , THR A:129 , LEU A:131 , SER A:136 , SER A:139 , LYS A:141 , ASN A:151 , GLN A:176 , HOH A:669 , HOH A:696 , HOH A:708 , HOH A:728 , HOH A:751BINDING SITE FOR RESIDUE NAD A 603
07AC7SOFTWAREASP A:135 , GLU A:183 , LYS A:186 , LYS A:225 , GLU A:235 , PHE A:242 , GLU A:243 , HIS A:246 , HIS A:262 , CO A:601 , PO4 A:608 , HOH A:616 , HOH A:695BINDING SITE FOR RESIDUE EXO A 607
08AC8SOFTWAREARG A:119 , ASP B:42 , GLY B:44 , VAL B:45 , PRO B:46 , ILE B:49 , GLU B:72 , LYS B:75 , GLY B:103 , GLY B:104 , LEU B:105 , ASN B:108 , THR B:128 , THR B:129 , LEU B:131 , SER B:136 , LYS B:150 , ASN B:151 , GLN B:176 , CAK B:609 , HOH B:673 , HOH B:693 , HOH B:697 , HOH B:738 , HOH B:745BINDING SITE FOR RESIDUE NAD B 604
09AC9SOFTWAREARG A:119 , ASP B:135 , LYS B:141 , ASN B:151 , GLU B:183 , LYS B:186 , LYS B:225 , GLU B:235 , PHE B:242 , HIS B:246 , HIS B:250 , HIS B:262 , CO B:602 , NAD B:604 , HOH B:635 , HOH B:701BINDING SITE FOR RESIDUE CAK B 609
10BC1SOFTWARETYR A:52 , ARG A:167 , ILE A:168 , GLU A:171BINDING SITE FOR RESIDUE MPD A 611
11BC2SOFTWAREASN B:278 , ASN B:281 , MET B:283BINDING SITE FOR RESIDUE MPD B 610

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:12
2B:7 -B:12

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GRU)

(-) 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:367
 aligned with DOIS_BACCI | Q9S5E2 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:367
                                    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       
           DOIS_BACCI     2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee..hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhh............eeee..eee..ee........eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gru A   2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
                                    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       


Chain B from PDB  Type:PROTEIN  Length:360
 aligned with DOIS_BACCI | Q9S5E2 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:367
                                    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       
           DOIS_BACCI     2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee..hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhh.-------...eeeee.eee..ee.......eeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gru B   2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDN-------DEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
                                    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       
                                                                                                                                                                                                                                                                                                                                                         321     329
   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  (0, 0)

(no "SCOP Domain" information available for 2GRU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DOIS_BACCI | Q9S5E2)
molecular function
    GO:0016838    carbon-oxygen lyase activity, acting on phosphates    Catalysis of the cleavage of a carbon-oxygen bond by elimination of a phosphate.
    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.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).

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