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(-) Description

Title :  2.5 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF OF HUMAN 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE IN COMPLEX WITH DIPICOLINIC ACID
 
Authors :  L. Huo, A. Liu
Date :  18 Dec 12  (Deposition) - 21 May 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Tim-Barrel, Decarboxylation, Metal-Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Huo, F. Liu, H. Iwaki, T. Li, Y. Hasegawa, A. Liu
Human Alpha-Amino-Beta-Carboxymuconate-Epsilon-Semialdehyde Decarboxylase (Acmsd): A Structural And Mechanistic Unveiling.
Proteins V. 83 178 2015
PubMed-ID: 25392945  |  Reference-DOI: 10.1002/PROT.24722

(-) Compounds

Molecule 1 - 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
    Chains: A, B, C, D, E, F
    EC Number: 4.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Gene: ACMSD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PICOLINATE CARBOXYLASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A    F
Biological Unit 2 (1x):  BC   
Biological Unit 3 (1x):    DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1PDC6Ligand/IonPYRIDINE-2,6-DICARBOXYLIC ACID
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PDC2Ligand/IonPYRIDINE-2,6-DICARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PDC2Ligand/IonPYRIDINE-2,6-DICARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1PDC2Ligand/IonPYRIDINE-2,6-DICARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:6 , HIS A:8 , HIS A:174 , ASP A:291 , PDC A:402BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:8 , ARG A:47 , VAL A:76 , PRO A:77 , HIS A:174 , TRP A:191 , ASP A:291 , PHE A:294 , LEU A:296 , ZN A:401BINDING SITE FOR RESIDUE PDC A 402
03AC3SOFTWAREHIS B:6 , HIS B:8 , HIS B:174 , ASP B:291 , PDC B:402BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREHIS B:8 , ARG B:47 , VAL B:76 , PRO B:77 , VAL B:78 , HIS B:174 , TRP B:191 , ASP B:291 , PHE B:294 , ZN B:401 , HOH B:561BINDING SITE FOR RESIDUE PDC B 402
05AC5SOFTWAREHIS C:6 , HIS C:8 , HIS C:174 , ASP C:291 , PDC C:402BINDING SITE FOR RESIDUE ZN C 401
06AC6SOFTWAREHIS C:8 , ARG C:47 , VAL C:76 , PRO C:77 , VAL C:78 , HIS C:174 , TRP C:191 , ASP C:291 , PHE C:294 , ZN C:401 , HOH C:528 , HOH C:533BINDING SITE FOR RESIDUE PDC C 402
07AC7SOFTWAREHIS D:6 , HIS D:8 , HIS D:174 , ASP D:291 , PDC D:402BINDING SITE FOR RESIDUE ZN D 401
08AC8SOFTWAREHIS D:8 , PHE D:46 , ARG D:47 , PRO D:77 , HIS D:174 , TRP D:191 , MET D:195 , HIS D:224 , ASP D:291 , LEU D:296 , ZN D:401BINDING SITE FOR RESIDUE PDC D 402
09AC9SOFTWAREHIS E:6 , HIS E:8 , HIS E:174 , ASP E:291 , PDC E:402BINDING SITE FOR RESIDUE ZN E 401
10BC1SOFTWAREARG E:47 , VAL E:76 , PRO E:77 , HIS E:174 , TRP E:188 , TRP E:191 , ASP E:291 , PHE E:294 , LEU E:296 , ZN E:401BINDING SITE FOR RESIDUE PDC E 402
11BC2SOFTWAREHIS F:6 , HIS F:8 , HIS F:174 , ASP F:291 , PDC F:402BINDING SITE FOR RESIDUE ZN F 401
12BC3SOFTWAREHIS F:8 , ARG F:47 , VAL F:76 , PRO F:77 , HIS F:174 , TRP F:191 , ASP F:291 , PHE F:294 , LEU F:296 , ZN F:401 , HOH F:505BINDING SITE FOR RESIDUE PDC F 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IH3)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:292 -Pro A:293
2Tyr B:292 -Pro B:293
3Tyr C:292 -Pro C:293
4Tyr D:292 -Pro D:293
5Tyr E:292 -Pro E:293
6Tyr F:292 -Pro F:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IH3)

(-) Exons   (0, 0)

(no "Exon" information available for 4IH3)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhh....eeee.....eeeeee..eeeeeee.hhhhhhhhhhhhhhh...eeeeee.hhhh....hhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhh..........hhhhh....eee....hhhhhhhhhhhhh...ee........................hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 A   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  


Chain B from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh....eeeee....eeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhh..eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee....hhhhhhhhhhhhh...ee..............hhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 B   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  


Chain C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh.....eee.......eeee..eeeee.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhh..eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....eee....hhhhhhhhhhhhh...ee..............hhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 C   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  


Chain D from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh....eeeeeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhh...eeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhh..eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee....hhhhhhhhhhhh....ee..............hhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 D   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  


Chain E from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh....eeeee.....eeeee..eeeeeehhhhhhhhhhhhhhhhh...eeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhhh.eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eee....hhhhhhhhhhhhh...ee..............hhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 E   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  


Chain F from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhh....eeeee....eeeeee...eeeeee.hhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhh..eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee....hhhhhhhhhhhhhhh.ee..............hhhhhhh.....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ih3 F   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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
   Legend:   → Mismatch (orange background)
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  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 4IH3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IH3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IH3)

(-) Gene Ontology  (16, 16)

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 Related Entries

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

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        ACMSD_HUMAN | Q8TDX5: 2wm1 4igm 4ign 4ofc

(-) Related Entries Specified in the PDB File

4ifk 4ifo 4ifr 4ig2