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(-) Description

Title :  CMCI-N160 IN COMPLEX WITH SAM
 
Authors :  L. M. Oster, D. R. Lester, A. Terwisscha Van Scheltinga, M. Svenda, C. I. Andersson
Date :  10 Mar 05  (Deposition) - 09 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Cephamycin Biosynthesis, Porin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Oster, D. R. Lester, A. Terwisscha Van Scheltinga, M. Svenda, M. Van Lun, C. Genereux, I. Andersson
Insights Into Cephamycin Biosynthesis: The Crystal Structure Of Cmci From Streptomyces Clavuligerus
J. Mol. Biol. V. 358 546 2006
PubMed-ID: 16527306  |  Reference-DOI: 10.1016/J.JMB.2006.02.004

(-) Compounds

Molecule 1 - CEPHALOSPORIN HYDROXYLASE CMCI
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STREPTOMYCES CLAVULIGERUS
    Organism Taxid: 1901

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SAM6Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:65 , GLU A:87 , GLY A:89 , TYR A:91 , SER A:95 , ASP A:116 , ARG A:117 , ARG A:121 , ASP A:138 , CYS A:139 , ASN A:160BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWARELEU B:18 , LEU B:64 , LYS B:65 , GLU B:87 , GLY B:89 , VAL B:90 , TYR B:91 , SER B:95 , ASP B:116 , ARG B:117 , ARG B:121 , GLY B:137 , ASP B:138 , CYS B:139 , ASN B:160 , ALA B:163BINDING SITE FOR RESIDUE SAM B 301
3AC3SOFTWARELEU C:64 , LYS C:65 , GLU C:87 , GLY C:89 , VAL C:90 , TYR C:91 , ASN C:92 , SER C:95 , ASP C:116 , ARG C:117 , ARG C:121 , GLY C:137 , ASP C:138 , CYS C:139 , ASN C:160 , ALA C:161 , ALA C:163BINDING SITE FOR RESIDUE SAM C 301
4AC4SOFTWARELEU D:18 , LEU D:64 , LYS D:65 , GLU D:87 , GLY D:89 , VAL D:90 , TYR D:91 , ASP D:116 , ARG D:117 , ARG D:121 , ASP D:138 , CYS D:139 , ASN D:160 , ALA D:161 , HOH D:2025BINDING SITE FOR RESIDUE SAM D 301
5AC5SOFTWARELEU E:18 , LEU E:64 , LYS E:65 , GLU E:87 , GLY E:89 , TYR E:91 , SER E:95 , ASP E:116 , ARG E:117 , ARG E:121 , ASP E:138 , CYS E:139 , ASN E:160 , ALA E:161 , ALA E:163BINDING SITE FOR RESIDUE SAM E 301
6AC6SOFTWAREGLY F:17 , GLY F:89 , ASP F:116 , ARG F:117 , ARG F:121 , GLY F:137 , CYS F:139 , ASN F:160 , HIS F:162BINDING SITE FOR RESIDUE SAM F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BM9)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1His A:153 -Pro A:154
2His B:153 -Pro B:154
3His C:153 -Pro C:154
4His D:153 -Pro D:154
5His E:153 -Pro E:154
6His F:153 -Pro F:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BM9)

(-) Exons   (0, 0)

(no "Exon" information available for 2BM9)

(-) 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:232
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
         B5GLB3_STRC2     2 NDYSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
               SCOP domains d2bm9a_ A: Cephalosporin hydroxylase CmcI                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh..................eee.hhhhhh............ee..ee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh....eeeee.........hhhhh..ee........hhhhhh.......eeeee.....hhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhh...eeeehhhhh........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 A   2 NDYSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
         B5GLB3_STRC2     4 YSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVAA 234
               SCOP domains d2bm9b_ B: Cephalosporin hydroxylase CmcI                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eee.hhhhhh............ee..ee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeeee........hhhhh..eeeee....hhhhhhhhh.....eeeee....hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh....eeeehhhhh........eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 B   4 YSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVAA 234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 


Chain C from PDB  Type:PROTEIN  Length:231
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
         B5GLB3_STRC2     3 DYSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
               SCOP domains d2bm9c_ C: Cephalosporin hydroxylase CmcI                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..................eehhhhhhhh............ee..ee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...eeeeee........hhhhh..eeeee.....hhhhhh.......eeeee....hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhhhh..eeee.............eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 C   3 DYSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 


Chain D from PDB  Type:PROTEIN  Length:232
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
         B5GLB3_STRC2     2 NDYSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
               SCOP domains d2bm9d_ D: Cephalosporin hydroxylase CmcI                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhh..................eee.hhhhhh............ee..ee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh....eeeeee.hhhhh..hhhhh..eeeee.....hhhhhh.......eeeee......hhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh.....eeehhhhh........eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 D   2 NDYSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  


Chain E from PDB  Type:PROTEIN  Length:231
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
         B5GLB3_STRC2     3 DYSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
               SCOP domains d2bm9e_ E: Cephalosporin hydroxylase CmcI                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................eee.hhhhhh.....................hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...eeeeee...............eeeee.....hhhhhh.......eeeee....hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhhh....eee......hhhhh..eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 E   3 DYSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVA 233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 


Chain F from PDB  Type:PROTEIN  Length:232
 aligned with B5GLB3_STRC2 | B5GLB3 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
         B5GLB3_STRC2     3 DYSRQNFLDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDDAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLLSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVAA 234
               SCOP domains d2bm9f_ F: Cephalosporin hydroxylase CmcI                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..................eee.hhh..............ee....ee..hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhh....eee...........hhhhh............hhhhhh.......eeeee....hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhhh...eeee.............eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm9 F   3 DYSRQNFQDLNLFRGLGEDPAYHPPVLTDRPRDWPLDRWAEAPRDLGYSDFSPYQWRGLRMLKDPDTQAVYHDMLWELRPRTIVELGVYNGGSLAWFRDLTKIMGIDCQVIGIDRDLSRCQIPASDMENITLHQGDCSDLTTFEHLREMAHPLIFIDNAHANTFNIMKWAVDHLLEEGDYFIIEDMIPYWYRYAPQLFSEYLGAFRDVLSMDMLYANASSQLDRGVLRRVAA 234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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  (1, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BM9)

(-) Gene Ontology  (6, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (B5GLB3_STRC2 | B5GLB3)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
    GO:0008610    lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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  2bm9
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        B5GLB3_STRC2 | B5GLB3: 2bm8 2br3 2br4 2br5

(-) Related Entries Specified in the PDB File

2bm8 CMCI-N160 APO-STRUCTURE
2br3 CMCI-D160 MG
2br4 CMCI-D160 MG-SAM
2br5 CMCI-N160 SAH