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(-) Description

Title :  CRYSTAL STRUCTURE OF LYSINE 5,6-AMINOMUTASE IN COMPLEX WITH PLP, COBALAMIN, AND 5'-DEOXYADENOSINE
 
Authors :  F. Berkovitch, E. Behshad, K. H. Tang, E. A. Enns, P. A. Frey, C. L. Drenna
Date :  15 Oct 04  (Deposition) - 09 Nov 04  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim Barrel, Rossmann Domain, Plp, Cobalamin, B12, 5'-Deoxyadenosine, Radical, Mutase, Adenosylcobalamin, Conformational Change, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Berkovitch, E. Behshad, K. H. Tang, E. A. Enns, P. A. Frey, C. L. Drennan
A Locking Mechanism Preventing Radical Damage In The Absenc Of Substrate, As Revealed By The X-Ray Structure Of Lysine 5, 6-Aminomutase.
Proc. Natl. Acad. Sci. Usa V. 101 15870 2004
PubMed-ID: 15514022  |  Reference-DOI: 10.1073/PNAS.0407074101

(-) Compounds

Molecule 1 - D-LYSINE 5,6-AMINOMUTASE ALPHA SUBUNIT
    Chains: A
    EC Number: 5.4.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: KAMDE
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Gene: KAMDE
    Organism Scientific: CLOSTRIDIUM STICKLANDII
    Organism Taxid: 1511
 
Molecule 2 - D-LYSINE 5,6-AMINOMUTASE BETA SUBUNIT
    Chains: B
    EC Number: 5.4.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: KAMDE
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Gene: KAMDE
    Organism Scientific: CLOSTRIDIUM STICKLANDII
    Organism Taxid: 1511

 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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2B121Ligand/IonCOBALAMIN
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2B122Ligand/IonCOBALAMIN
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:516 , THR B:130 , ASP B:131 , ALA B:132 , HIS B:133 , THR B:134 , VAL B:135 , GLY B:136 , ILE B:140 , TYR B:146 , LEU B:185 , VAL B:186 , SER B:187 , VAL B:190 , THR B:191 , GLN B:192 , LEU B:219 , GLY B:221 , GLY B:222 , PRO B:223 , PHE B:239 , GLY B:240 , PRO B:241 , ARG B:243 , PHE B:244 , VAL B:248 , 5AD B:500BINDING SITE FOR RESIDUE B12 B 800
2AC2SOFTWAREARG A:184 , THR A:186 , GLY A:187 , GLN A:188 , SER A:189 , TYR A:236 , SER A:238 , TYR A:263 , ARG A:268 , ASN A:299 , LYS B:144BINDING SITE FOR RESIDUE PLP B 801
3AC3SOFTWAREASP A:54 , GLU A:55 , VAL A:56 , TYR A:193 , B12 B:800BINDING SITE FOR RESIDUE 5AD B 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B12_BINDINGPS51332 B12-binding domain profile.KAMED_ACESD120-262  1B:120-261
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B12_BINDINGPS51332 B12-binding domain profile.KAMED_ACESD120-262  2B:120-261

(-) Exons   (0, 0)

(no "Exon" information available for 1XRS)

(-) 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:516
 aligned with KAMDD_ACESD | E3PRJ5 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:516
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513      
          KAMDD_ACESD     4 VESKLNLDFNLVEKARAKAKAIAIDTQEFIEKHTTVTVERAVCRLLGIDGVDTDEVPLPNIVVDHIKENNGLNLGAAMYIANAVLNTGKTPQEIAQAISAGELDLTKLPMKDLFEVKTKALSMAKETVEKIKNNRSIRESRFEEYGDKSGPLLYVIVATGNIYEDITQAVAAAKQGADVIAVIRTTGQSLLDYVPYGATTEGFGGTYATQENFRLMREALDKVGAEVGKYIRLCNYCSGLCMPEIAAMGAIERLDVMLNDALYGILFRDINMQRTMIDQNFSRIINGFAGVIINTGEDNYLTTADAFEEAHTVLASQFINEQFALLAGLPEEQMGLGHAFEMDPELKNGFLYELSQAQMAREIFPKAPLKYMPPTKFMTGNIFKGHIQDALFNMVTIMTNQRIHLLGMLTEALHTPFMSDRALSIENAQYIFNNMESISEEIQFKEDGLIQKRAGFVLEKANELLEEIEQLGLFDTLEKGIFGGVKRPKDGGKGLNGVVSKDENYYNPFVELMLNK 519
               SCOP domains d1xrsa_ A: D-lysine 5,6-aminomutase alpha subunit, KamD                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xrsA00 A:1-516 D-lysine 5,6-aminomutase alpha subunit. Chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhh..........hhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhh...eeee....hhhhh.................hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh..eee...hhhhhhhh.hhhhhhhhhhhhhhhhhhh..eee..hhhhhh......hhhhhhhhhhhhhhhhhhh..hhh.ee.eee........hhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhh.eee......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xrs A   1 MESKLNLDFNLVEKARAKAKAIAIDTQEFIEKHTTVTVERAVCRLLGIDGVDTDEVPLPNIVVDHIKENNGLNLGAAMYIANAVLNTGKTPQEIAQAISAGELDLTKLPMKDLFEVKTKALSMAKETVEKIKNNRSIRESRFEEYGDKSGPLLYVIVATGNIYEDITQAVAAAKQGADVIAVIRTTGQSLLDYVPYGATTEGFGGTYATQENFRLMREALDKVGAEVGKYIRLCNYCSGLCMPEIAAMGAIERLDVMLNDALYGILFRDINMQRTMIDQNFSRIINGFAGVIINTGEDNYLTTADAFEEAHTVLASQFINEQFALLAGLPEEQMGLGHAFEMDPELKNGFLYELSQAQMAREIFPKAPLKYMPPTKFMTGNIFKGHIQDALFNMVTIMTNQRIHLLGMLTEALHTPFMSDRALSIENAQYIFNNMESISEEIQFKEDGLIQKRAGFVLEKANELLEEIEQLGLFDTLEKGIFGGVKRPKDGGKGLNGVVSKDENYYNPFVELMLNK 516
                                    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      


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with KAMED_ACESD | E3PRJ4 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:229
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
          KAMED_ACESD    33 KVQLSFTLPLKNNERSAEAAKQIALKMGLEEPSVVMQQSLDEEFTFFVVYGNFVQSVNYNEIHVEAVNSEILSMEETDEYIKENIGRKIVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKAVELEADVLLVSQTVTQKNVHIQNMTHLIELLEAEGLRDRFVLLCGGPRINNEIAKELGYDAGFGPGRFADDVATFAVKTLNDRMN 261
               SCOP domains d1xrsb2 B:33-84                                     -----------------d1xrsb1 B:102-261 D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain                                                                                  SCOP domains
               CATH domains 1xrsB01 B:33-84                                     -----------------1xrsB02 B:102-261  [code=3.40.50.280, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhh......eeeeeeeee..eeeeeeee.-----------------...hhhhhhhhhhhhh...eeeeeee......hhhhhhhhh........hhhhh..eeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh.hhhhheeeee....hhhhhhh....eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------B12_BINDING  PDB: B:120-261 UniProt: 120-262                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xrs B  33 KVQLSFTLPLKNNERSAEAAKQIALKMGLEEPSVVMQQSLDEEFTFFVVYGN-----------------EILSMEETDEYIKENIGRKIVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKAVELEADVLLVSQTVTQKNVHIQNMTHLIELLEAEGLRDRFVLLCGGPRINNEIAKELGYDAGFGPGRFADDVATFAVKTLNDRMN 261
                                    42        52        62        72        82 |       -       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252         
                                                                              84               102
   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  (3, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XRS)

(-) Gene Ontology  (7, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (KAMDD_ACESD | E3PRJ5)
molecular function
    GO:0047826    D-lysine 5,6-aminomutase activity    Catalysis of the reaction: D-lysine = 2,5-diaminohexanoate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Chain B   (KAMED_ACESD | E3PRJ4)
molecular function
    GO:0047826    D-lysine 5,6-aminomutase activity    Catalysis of the reaction: D-lysine = 2,5-diaminohexanoate.
    GO:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.

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