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(-) Description

Title :  CRYSTAL STRUCTURE OF A NIMC/NIMA FAMILY PROTEIN (CA_C2569) FROM CLOSTRIDIUM ACETOBUTYLICUM AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Sep 06  (Deposition) - 10 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nimc/Nima Family Protein (Np_349178. 1) From Clostridium Acetobutylicum At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NIMC/NIMA FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_349178.1
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 1488

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO43Ligand/IonSULFATE ION
5UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:72 , ARG B:27 , LYS B:48 , CYS B:49 , HOH B:139 , HOH B:212 , HOH B:246 , HOH B:264BINDING SITE FOR RESIDUE SO4 B 132
2AC2SOFTWAREHIS A:-10 , HIS A:-7 , TYR A:-3 , VAL A:93 , PRO A:94 , SER A:95BINDING SITE FOR RESIDUE SO4 A 132
3AC3SOFTWAREHIS B:-8 , HIS B:-7 , GLU B:-6 , ASN B:44 , LYS B:47 , HOH B:242BINDING SITE FOR RESIDUE SO4 B 133
4AC4SOFTWAREASN A:-5 , HIS A:-8 , VAL A:13 , ARG A:27 , PRO A:28 , PHE A:29 , GLY A:30 , ALA A:31 , VAL A:42 , SER A:43 , LYS A:47 , LYS A:48 , CYS A:49 , UNL A:340 , HOH A:342 , HOH A:343 , HOH A:374 , HOH A:379 , HOH A:390 , HOH A:470 , TRP B:70 , ARG B:72BINDING SITE FOR RESIDUE FMN A 339
5AC5SOFTWAREASN A:-5 , LEU A:-4 , LYS A:47 , LEU A:96 , MSE A:99 , TYR A:100 , FMN A:339 , HOH A:455BINDING SITE FOR RESIDUE UNL A 340
6AC6SOFTWARELYS B:9 , GLY B:30 , ALA B:31 , VAL B:32 , HOH B:224 , HOH B:267BINDING SITE FOR RESIDUE EDO B 134

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IG6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IG6)

(-) Exons   (0, 0)

(no "Exon" information available for 2IG6)

(-) 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:143
 aligned with Q97G05_CLOAB | Q97G05 from UniProtKB/TrEMBL  Length:131

    Alignment length:143
                                        1                                                                                                                                  
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128   
         Q97G05_CLOAB     - ------------MKRALEFLKECGVFYLATNEGDQPRVRPFGAVFEYEGKLYIVSNNTKKCFKQMIQNPKVEISGMNKKGQWIRLTGEVANDDRREVKELALEAVPSLKNMYSVDDGIFAVLYFTKGEGTICSFKGENETFSL 131
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ig6A00 A:-11-131 Electron Transport, Fmn-binding Protein; Chain A                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eee..eeeeeee..hhhhhhhhhh.eeeeeee.....eeeeeeeeee..hhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeee......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ig6 A -11 HHHHHENLYFQGmKRALEFLKECGVFYLATNEGDQPRVRPFGAVFEYEGKLYIVSNNTKKCFKQmIQNPKVEISGmNKKGQWIRLTGEVANDDRREVKELALEAVPSLKNmYSVDDGIFAVLYFTKGEGTICSFKGENETFSL 131
                                    -2  |      8        18        28        38        48    |   58     |  68        78        88        98|      108       118       128   
                                        1-MSE                                              53-MSE     64-MSE                             99-MSE                            


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with Q97G05_CLOAB | Q97G05 from UniProtKB/TrEMBL  Length:131

    Alignment length:141
                                      1                                                                                                                                  
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130 
         Q97G05_CLOAB     - ----------MKRALEFLKECGVFYLATNEGDQPRVRPFGAVFEYEGKLYIVSNNTKKCFKQMIQNPKVEISGMNKKGQWIRLTGEVANDDRREVKELALEAVPSLKNMYSVDDGIFAVLYFTKGEGTICSFKGENETFSL 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ig6B00 B:-9-131 Electron Transport, Fmn-binding Protein; Chain A                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eee..eeeeeee..hhhhhhhhhh.eeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeeee..--eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ig6 B  -9 HHHENLYFQGmKRALEFLKECGVFYLATNEGDQPRVRPFGAVFEYEGKLYIVSNNTKKCFKQmIQNPKVEISGmNKKGQWIRLTGEVANDDRREVKELALEAVPSLKNmYSVDDGIFAVLYFTKGEGTICSFK--NETFSL 131
                                     0|       10        20        30        40        50  |     60   |    70        80        90       100       110       120  |  | 130 
                                      1-MSE                                              53-MSE     64-MSE                             99-MSE                 123  |     
                                                                                                                                                                 126
   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 2IG6)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IG6)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97G05_CLOAB | Q97G05)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.

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