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Title :   CRYSTAL STRUCTURE OF MONO-ZINC FORM OF SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE

Authors :   B. P. Nocek, D. M. Gillner, R. C. Holz, A. Joachimiak, Midwest Center F Structural Genomics (Mcsg)

Date :   27 Aug 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dape, Succinyl-Diaminopimelate Desuccinylase, Zn-Binding, Metallopeptidase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Amino-Acid Biosynthesis, Cobalt, Diaminopimelate Biosynthesis, Hydrolase, Lysine Biosynthesis, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. P. Nocek, D. M. Gillner, Y. Fan, R. C. Holz, A. Joachimiak
Structural Basis For Catalysis By The Mono- And Dimetalated Forms Of The Dape-Encoded N-Succinyl-L, L-Diaminopimelic Aci Desuccinylase.
J. Mol. Biol. V. 397 617 2010
PubMed-ID: 20138056 | Reference-DOI: 10.1016/J.JMB.2010.01.062

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DAPE, HI0102
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	71421
	Strain	:	RD KW20
	Synonym	:	SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE AMIDOHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:67 , ASP A:100 , GLU A:163 , HOH A:572	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	ARG A:178 , ARG A:179 , GLY A:322 , HOH A:552 , HOH A:580 , HOH A:587 , HOH A:588	BINDING SITE FOR RESIDUE SO4 A 378
3	AC3	SOFTWARE	HIS B:67 , ASP B:100 , GLU B:163 , HOH B:420	BINDING SITE FOR RESIDUE ZN B 1001
4	AC4	SOFTWARE	ARG B:178 , ARG B:179 , ARG B:258 , GLY B:322 , HOH B:419 , HOH B:491	BINDING SITE FOR RESIDUE SO4 B 378

(no "SS Bond" information available for 3ISZ)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:19	-	Pro A:20
2	Glu A:59	-	Pro A:60
3	Asp A:100	-	Met A:101
4	Ser B:19	-	Pro B:20
5	Glu B:59	-	Pro B:60
6	Asp B:100	-	Met B:101

(no "SAP(SNP)/Variant" information available for 3ISZ)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARGE_DAPE_CPG2_1	PS00758	ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.	DAPE_HAEIN	62-71	2	A:62-71 B:62-71
2	ARGE_DAPE_CPG2_2	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.	DAPE_HAEIN	98-137	2	A:98-137 B:98-137

(no "Exon" information available for 3ISZ)

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:369
 aligned with DAPE_HAEIN | P44514 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:376
                                    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      
           DAPE_HAEIN     1 MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQGHVAYPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNVIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLTKPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLLD 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iszA01 A:1-178,A:293-376 Zn peptidases                                                                                                                                           3iszA02 A:179       -292  [code=3.30.70.360, no name defined]                                                     3iszA01 A:1-178,A:293-376 Zn peptidases                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeee.......eeeeeee....eeeeeee.......hhhhh........ee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhh.....eeee...........eeeeee.eeeeeeeeee..-------hhhhhhhhhhhhhhhhhhhh............eeeeeeeee..........eeeeeeeeee....hhhhhhhhhhhhhhhh...eeeeeee....ee...hhhhhhhhhhhhhhhh...eeee.....hhhhhhh...eeee.............eeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------ARGE_DAPE_--------------------------ARGE_DAPE_CPG2_2  PDB: A:98-137         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isz A   1 MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGI-------HLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNVIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLTKPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLLD 376
                                    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      
                                                                                                                                                                                                                        191     199

Chain B from PDB  Type:PROTEIN  Length:366
 aligned with DAPE_HAEIN | P44514 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:376
                                    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      
           DAPE_HAEIN     1 MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQGHVAYPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNVIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLTKPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLLD 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iszB01 B:1-178,B:293-376 Zn peptidases                                                                                                                                           3iszB02 B:179-     292  [code=3.30.70.360, no name defined]                                                       3iszB01 B:1-178,B:293-376 Zn peptidases                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeee.......eeeeee.....eeeeeee.......hhhhh........ee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhh.....eeee...........eeeeee.eeeeeeeeee...-----.hhhhhhhhhhhhhhhhhh..............eeeeeeeee.-----....eeeeeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeeee..ee...hhhhhhhhhhhhhhhh...eeee.....hhhhhhh...eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------ARGE_DAPE_--------------------------ARGE_DAPE_CPG2_2  PDB: B:98-137         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isz B   1 MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQ-----PHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAG-----VIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLTKPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVNECVSVEDLGKCGEIYHKMLVNLLD 376
                                    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      
                                                                                                                                                                                                                         192   198                                       240   246

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 '\|'

(no "SCOP Domain" information available for 3ISZ)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.360, no name defined] (23)

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: rd kw20. (1)

1a	3iszA02	A:179-292
1b	3iszB02	B:179-292

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: Zn peptidases (137)

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: rd kw20. (1)

2a	3iszA01	A:1-178,A:293-376
2b	3iszB01	B:1-178,B:293-376

(no "Pfam Domain" information available for 3ISZ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DAPE_HAEIN | P44514)

molecular function
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0009014	succinyl-diaminopimelate desuccinylase activity	Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H(2)O = LL-2,6-diaminopimelate + succinate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	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.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Glu A:59 - Pro A:60	[ RasMol ]
		Glu B:59 - Pro B:60	[ RasMol ]
		Ser A:19 - Pro A:20	[ RasMol ]
		Ser B:19 - Pro B:20	[ RasMol ]

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	DAPE_HAEIN \| P44514	:	3ic1 4h2k

3ic1	CRYSTAL STRUCTURE OF ZINC-BOUND SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE RELATED ID: APC61309 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

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